rs4938638

Variant names:

• chr11-119204719-G-A
• rs4938638

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 0.622 in 151,098 control chromosomes in the GnomAD database, including 30,842 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 (30842 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.748
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 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: 0.622 AC: 93924 AN: 150980 Hom.: 30794 Cov.: 31

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.622 AC: 94027 AN: 151098 Hom.: 30842 Cov.: 31 AF XY: 0.626 AC XY: 46225 AN XY: 73824

African (AFR) AF: 0.814 AC: 33097 AN: 40654

American (AMR) AF: 0.464 AC: 7060 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2215 AN: 3466

East Asian (EAS) AF: 0.880 AC: 4552 AN: 5174

South Asian (SAS) AF: 0.767 AC: 3699 AN: 4822

European-Finnish (FIN) AF: 0.544 AC: 5742 AN: 10558

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35808 AN: 67930

Other (OTH) AF: 0.601 AC: 1256 AN: 2090

Alfa AF: 0.563 Hom.: 4401

Bravo AF: 0.621

Asia WGS AF: 0.807 AC: 2808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.8
DANN	Benign	0.60
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs4938638; hg19: chr11-119075429;