Genetic Variant ENST00000634870.1:n.3881G>A (chr1-94615889-C-T) – ACMG Classification: Benign (-12 pts)

Germline classification Cancer classification (beta)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BA1BP4_Strong

The ENST00000634870.1(SLC44A3-AS1):n.3881G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a cumulative frequency of 0.376 (AC=57,194) in the gnomAD database across 152,036 control chromosomes, including 10,805 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.489. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.38 ( 10804 hom., cov: 32)

Exomes 𝑓: 0.50 ( 1 hom. )

Consequence

SLC44A3-AS1
ENST00000634870.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.96

Publications

7 publications found

Variant links:

Genes affected

SLC44A3-AS1 (HGNC:):

SLC44A3-AS1 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000634870.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript

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

BP4

Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).

BA1

GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.4889 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634870.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
SLC44A3-AS1	ENST00000634870.1	TSL:5	n.3881G>A	non_coding_transcript_exon	Exon 6 of 6
SLC44A3-AS1	ENST00000414374.2	TSL:3	n.439-29127G>A	intron	N/A
ENSG00000301906	ENST00000782778.1		n.342-19902C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.376

AC:

57167

AN:

151912

Hom.:

10805

Cov.:

show subpopulations

Gnomad AFR

AF:

0.354

Gnomad AMI

AF:

0.347

Gnomad AMR

AF:

0.384

Gnomad ASJ

AF:

0.391

Gnomad EAS

AF:

0.505

Gnomad SAS

AF:

0.381

Gnomad FIN

AF:

0.378

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.378

Gnomad OTH

AF:

0.371

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.376

AC:

57192

AN:

152032

Hom.:

10804

Cov.:

AF XY:

0.380

AC XY:

28225

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.353

AC:

14644

AN:

41450

American (AMR)

AF:

0.384

AC:

5868

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.391

AC:

1358

AN:

3470

East Asian (EAS)

AF:

0.505

AC:

2612

AN:

5172

South Asian (SAS)

AF:

0.382

AC:

1839

AN:

4820

European-Finnish (FIN)

AF:

0.378

AC:

3989

AN:

10544

Middle Eastern (MID)

AF:

0.412

AC:

121

AN:

294

European-Non Finnish (NFE)

AF:

0.378

AC:

25667

AN:

67984

Other (OTH)

AF:

0.370

AC:

779

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1870

3740

5609

7479

9349

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

560

1120

1680

2240

2800

<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:

0.392

Hom.:

14554

Bravo

AF:

0.374

Asia WGS

AF:

0.429

AC:

1492

AN:

3478

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.514

AC:

63061

AN:

122802

Turkish Variome

AF:

0.414

AC:

639

AN:

1544

Hom.:

140

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.482

AC:

4321

AN:

8960

Hom.:

1038

ABraOM SABE-WGS-1171

AF:

0.374

AC:

875

AN:

2342

Hom.:

172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.23

(source)

DANN

Benign

0.35

PhyloP100

-4.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Local populations

ClinVar

Computational scores

Splicing

Publications

Other links and lift over