Genetic Variant SLC44A3:c.1482+95G>T (chr1-94867512-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001114106.3(SLC44A3):c.1482+95G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 874,770 control chromosomes in the GnomAD database, including 214,520 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 0.62 ( 31236 hom., cov: 32)

Exomes 𝑓: 0.71 ( 183284 hom. )

Consequence

SLC44A3
NM_001114106.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.259

Publications

7 publications found

Variant links:

Genes affected

SLC44A3 (HGNC:28689): (solute carrier family 44 member 3) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC44A3 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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001114106.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC44A3	NM_001114106.3	MANE Select	c.1482+95G>T	intron	N/A	NP_001107578.1
SLC44A3	NM_001258340.2		c.1479+95G>T	intron	N/A	NP_001245269.1
SLC44A3	NM_001258341.2		c.1383+95G>T	intron	N/A	NP_001245270.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC44A3	ENST00000271227.11	TSL:1 MANE Select	c.1482+95G>T	intron	N/A	ENSP00000271227.6
SLC44A3	ENST00000467909.5	TSL:1	c.1338+95G>T	intron	N/A	ENSP00000432789.1
SLC44A3	ENST00000475883.5	TSL:1	n.*1205+95G>T	intron	N/A	ENSP00000434457.1

Frequencies

GnomAD3 genomes

AF:

0.624

AC:

94850

AN:

151936

Hom.:

31205

Cov.:

show subpopulations

Gnomad AFR

AF:

0.393

Gnomad AMI

AF:

0.603

Gnomad AMR

AF:

0.665

Gnomad ASJ

AF:

0.686

Gnomad EAS

AF:

0.767

Gnomad SAS

AF:

0.683

Gnomad FIN

AF:

0.767

Gnomad MID

AF:

0.595

Gnomad NFE

AF:

0.715

Gnomad OTH

AF:

0.657

GnomAD4 exome

AF:

0.708

AC:

511949

AN:

722714

Hom.:

183284

AF XY:

0.708

AC XY:

260115

AN XY:

367154

show subpopulations

African (AFR)

AF:

0.379

AC:

6460

AN:

17064

American (AMR)

AF:

0.660

AC:

15280

AN:

23140

Ashkenazi Jewish (ASJ)

AF:

0.704

AC:

10354

AN:

14714

East Asian (EAS)

AF:

0.804

AC:

25020

AN:

31118

South Asian (SAS)

AF:

0.687

AC:

26835

AN:

39060

European-Finnish (FIN)

AF:

0.765

AC:

33928

AN:

44366

Middle Eastern (MID)

AF:

0.618

AC:

2398

AN:

3880

European-Non Finnish (NFE)

AF:

0.714

AC:

368582

AN:

516038

Other (OTH)

AF:

0.693

AC:

23092

AN:

33334

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

7240

14480

21720

28960

36200

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7648

15296

22944

30592

38240

<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:

0.624

AC:

94926

AN:

152056

Hom.:

31236

Cov.:

AF XY:

0.629

AC XY:

46743

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.393

AC:

16305

AN:

41444

American (AMR)

AF:

0.666

AC:

10177

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.686

AC:

2376

AN:

3466

East Asian (EAS)

AF:

0.768

AC:

3971

AN:

5172

South Asian (SAS)

AF:

0.682

AC:

3286

AN:

4820

European-Finnish (FIN)

AF:

0.767

AC:

8114

AN:

10574

Middle Eastern (MID)

AF:

0.588

AC:

173

AN:

294

European-Non Finnish (NFE)

AF:

0.715

AC:

48579

AN:

67976

Other (OTH)

AF:

0.661

AC:

1395

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1663

3325

4988

6650

8313

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

766

1532

2298

3064

3830

<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:

0.673

Hom.:

25308

Bravo

AF:

0.609

Asia WGS

AF:

0.721

AC:

2505

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.0

(source)

DANN

Benign

0.69

PhyloP100

-0.26

PromoterAI

-0.010

Neutral

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over