rs4238139

Variant names:

• chr13-30773452-G-A
• rs4238139

Your query was ambiguous. Multiple possible variants found:

• chr13-30773452-G-A
• chr13-30773452-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.696 in 152,142 control chromosomes in the GnomAD database, including 37,532 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 0.70 (37532 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105847 AN: 152024 Hom.: 37515 Cov.: 32

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.729

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.696 AC: 105902 AN: 152142 Hom.: 37532 Cov.: 32 AF XY: 0.698 AC XY: 51943 AN XY: 74374

African (AFR) AF: 0.549 AC: 22797 AN: 41496

American (AMR) AF: 0.796 AC: 12179 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2602 AN: 3470

East Asian (EAS) AF: 0.670 AC: 3469 AN: 5180

South Asian (SAS) AF: 0.714 AC: 3443 AN: 4820

European-Finnish (FIN) AF: 0.745 AC: 7878 AN: 10580

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51093 AN: 67988

Other (OTH) AF: 0.729 AC: 1539 AN: 2110

Alfa AF: 0.715 Hom.: 4892

Bravo AF: 0.697

Asia WGS AF: 0.715 AC: 2486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.48
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs4238139; hg19: chr13-31347589;