Genetic Variant NM_001029998.6:c.*302C>T (chr4-146256189-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001029998.6(SLC10A7):c.*302C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 408,904 control chromosomes in the GnomAD database, including 35,965 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.35 ( 11272 hom., cov: 33)

Exomes 𝑓: 0.43 ( 24693 hom. )

Consequence

SLC10A7
NM_001029998.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.76

Publications

17 publications found

Variant links:

Genes affected

SLC10A7 (HGNC:23088): (solute carrier family 10 member 7) Enables bile acid transmembrane transporter activity. Involved in several processes, including cellular calcium ion homeostasis; glycoprotein transport; and heparin biosynthetic process. Located in Golgi apparatus and endoplasmic reticulum. Is intrinsic component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC10A7 Gene-Disease associations (from GenCC):

short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics

SLC10A7 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC10A7	NM_001029998.6 link	c.*302C>T		3_prime_UTR_variant	Exon 12 of 12	ENST00000335472.12	NP_001025169.1	Q0GE19-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC10A7	ENST00000335472.12 link	c.*302C>T	3_prime_UTR_variant	Exon 12 of 12	1	NM_001029998.6	ENSP00000334594.8	Q0GE19-2
SLC10A7	ENST00000432059.6 link	c.*302C>T	3_prime_UTR_variant	Exon 11 of 11	1		ENSP00000411297.2	Q0GE19-3
SLC10A7	ENST00000693222.1 link	c.*302C>T	3_prime_UTR_variant	Exon 13 of 13			ENSP00000508969.1	A0A8I5QJB5

Frequencies

GnomAD3 genomes

AF:

0.353

AC:

53606

AN:

151986

Hom.:

11272

Cov.:

show subpopulations

Gnomad AFR

AF:

0.108

Gnomad AMI

AF:

0.582

Gnomad AMR

AF:

0.404

Gnomad ASJ

AF:

0.366

Gnomad EAS

AF:

0.326

Gnomad SAS

AF:

0.406

Gnomad FIN

AF:

0.434

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.473

Gnomad OTH

AF:

0.347

GnomAD4 exome

AF:

0.427

AC:

109661

AN:

256800

Hom.:

24693

Cov.:

AF XY:

0.427

AC XY:

58223

AN XY:

136242

show subpopulations

African (AFR)

AF:

0.100

AC:

736

AN:

7362

American (AMR)

AF:

0.397

AC:

3786

AN:

9540

Ashkenazi Jewish (ASJ)

AF:

0.363

AC:

2887

AN:

7960

East Asian (EAS)

AF:

0.285

AC:

4247

AN:

14914

South Asian (SAS)

AF:

0.402

AC:

12994

AN:

32338

European-Finnish (FIN)

AF:

0.431

AC:

6024

AN:

13968

Middle Eastern (MID)

AF:

0.370

AC:

411

AN:

1110

European-Non Finnish (NFE)

AF:

0.468

AC:

72482

AN:

154926

Other (OTH)

AF:

0.415

AC:

6094

AN:

14682

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

2830

5660

8490

11320

14150

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

336

672

1008

1344

1680

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.353

AC:

53618

AN:

152104

Hom.:

11272

Cov.:

AF XY:

0.352

AC XY:

26201

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.108

AC:

4488

AN:

41548

American (AMR)

AF:

0.404

AC:

6177

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.366

AC:

1267

AN:

3464

East Asian (EAS)

AF:

0.326

AC:

1688

AN:

5174

South Asian (SAS)

AF:

0.406

AC:

1960

AN:

4822

European-Finnish (FIN)

AF:

0.434

AC:

4582

AN:

10554

Middle Eastern (MID)

AF:

0.296

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.473

AC:

32108

AN:

67942

Other (OTH)

AF:

0.346

AC:

731

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1606

3211

4817

6422

8028

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

520

1040

1560

2080

2600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.427

Hom.:

28597

Bravo

AF:

0.338

Asia WGS

AF:

0.375

AC:

1300

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

(source)

DANN

Benign

0.75

PhyloP100

1.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over