rs4938637

Variant names:

• chr11-119204613-G-A
• rs4938637

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 0.0652 in 152,134 control chromosomes in the GnomAD database, including 619 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 0.065 (619 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.308 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: 0.0653 AC: 9926 AN: 152016 Hom.: 620 Cov.: 30

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.0561

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.0185

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0714

Gnomad OTH AF: 0.0825

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

GnomAD4 genome AF: 0.0652 AC: 9925 AN: 152134 Hom.: 619 Cov.: 30 AF XY: 0.0689 AC XY: 5125 AN XY: 74374

African (AFR) AF: 0.0159 AC: 659 AN: 41502

American (AMR) AF: 0.0561 AC: 856 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 388 AN: 3468

East Asian (EAS) AF: 0.214 AC: 1104 AN: 5164

South Asian (SAS) AF: 0.321 AC: 1550 AN: 4824

European-Finnish (FIN) AF: 0.0185 AC: 196 AN: 10610

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0714 AC: 4856 AN: 67986

Other (OTH) AF: 0.0863 AC: 182 AN: 2108

Alfa AF: 0.0692 Hom.: 1115

Bravo AF: 0.0608

Asia WGS AF: 0.239 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.6
DANN	Benign	0.46
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs4938637; hg19: chr11-119075323;