Genetic Variant ENSG00000287908:n.*144G>A (chr12-57619392-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 ENST00000474359.7(ENSG00000287908):n.*144G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 327,142 control chromosomes in the GnomAD database, including 20,275 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 0.32 ( 8836 hom., cov: 32)

Exomes 𝑓: 0.35 ( 11439 hom. )

Consequence

ENSG00000287908
ENST00000474359.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.49

Publications

25 publications found

Variant links:

COSMIC-nc: COSV54085899

Genes affected

ENSG00000287908 (HGNC:):

ENSG00000287908 links:

ENSG00000224713 (HGNC:41260):

ENSG00000224713 links:

SLC26A10P (HGNC:14470): (solute carrier family 26 member 10, pseudogene) Predicted to enable anion transmembrane transporter activity. Predicted to be involved in anion transport. Predicted to be active in basolateral plasma membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC26A10P links:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC101927583	NR_120450.1 link	n.2120+239C>T	intron_variant	Intron 2 of 3
SLC26A10P	NR_166678.1 link	n.-135G>A	upstream_gene_variant
SLC26A10P	NR_166679.1 link	n.-135G>A	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287908	ENST00000474359.7 link	n.*144G>A		non_coding_transcript_exon_variant	Exon 7 of 23	5		ENSP00000431994.2		E9PIH7
ENSG00000287908	ENST00000474359.7 link	n.*144G>A		3_prime_UTR_variant	Exon 7 of 23	5		ENSP00000431994.2		E9PIH7

Frequencies

GnomAD3 genomes

AF:

0.321

AC:

48743

AN:

152004

Hom.:

8841

Cov.:

show subpopulations

Gnomad AFR

AF:

0.167

Gnomad AMI

AF:

0.264

Gnomad AMR

AF:

0.337

Gnomad ASJ

AF:

0.540

Gnomad EAS

AF:

0.234

Gnomad SAS

AF:

0.234

Gnomad FIN

AF:

0.305

Gnomad MID

AF:

0.589

Gnomad NFE

AF:

0.411

Gnomad OTH

AF:

0.403

GnomAD4 exome

AF:

0.346

AC:

60533

AN:

175020

Hom.:

11439

Cov.:

AF XY:

0.334

AC XY:

31813

AN XY:

95300

show subpopulations

African (AFR)

AF:

0.159

AC:

674

AN:

4232

American (AMR)

AF:

0.290

AC:

2504

AN:

8634

Ashkenazi Jewish (ASJ)

AF:

0.523

AC:

2028

AN:

3880

East Asian (EAS)

AF:

0.228

AC:

1412

AN:

6204

South Asian (SAS)

AF:

0.244

AC:

9232

AN:

37838

European-Finnish (FIN)

AF:

0.325

AC:

2810

AN:

8654

Middle Eastern (MID)

AF:

0.547

AC:

705

AN:

1290

European-Non Finnish (NFE)

AF:

0.397

AC:

38009

AN:

95740

Other (OTH)

AF:

0.370

AC:

3159

AN:

8548

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1749

3497

5246

6994

8743

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

208

416

624

832

1040

<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:

0.320

AC:

48738

AN:

152122

Hom.:

8836

Cov.:

AF XY:

0.316

AC XY:

23504

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.167

AC:

6949

AN:

41512

American (AMR)

AF:

0.337

AC:

5143

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.540

AC:

1876

AN:

3472

East Asian (EAS)

AF:

0.234

AC:

1216

AN:

5186

South Asian (SAS)

AF:

0.233

AC:

1125

AN:

4820

European-Finnish (FIN)

AF:

0.305

AC:

3225

AN:

10562

Middle Eastern (MID)

AF:

0.588

AC:

173

AN:

294

European-Non Finnish (NFE)

AF:

0.411

AC:

27950

AN:

67990

Other (OTH)

AF:

0.399

AC:

841

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

1590

3179

4769

6358

7948

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

490

980

1470

1960

2450

<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:

0.406

Hom.:

19710

Bravo

AF:

0.316

Asia WGS

AF:

0.242

AC:

843

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.96

(source)

DANN

Benign

0.79

PhyloP100

-1.5

Splicing

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