rs4939008

Variant names:

• chr11-55922895-G-A
• rs4939008

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 0.623 in 151,760 control chromosomes in the GnomAD database, including 30,007 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 (30007 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.872
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 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: 0.623 AC: 94543 AN: 151642 Hom.: 29977 Cov.: 30

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.623 AC: 94604 AN: 151760 Hom.: 30007 Cov.: 30 AF XY: 0.619 AC XY: 45901 AN XY: 74162

African (AFR) AF: 0.675 AC: 27905 AN: 41322

American (AMR) AF: 0.533 AC: 8129 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2143 AN: 3466

East Asian (EAS) AF: 0.394 AC: 2025 AN: 5140

South Asian (SAS) AF: 0.431 AC: 2072 AN: 4810

European-Finnish (FIN) AF: 0.654 AC: 6878 AN: 10516

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43424 AN: 67950

Other (OTH) AF: 0.588 AC: 1240 AN: 2108

Alfa AF: 0.625 Hom.: 59036

Bravo AF: 0.617

Asia WGS AF: 0.411 AC: 1433 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	0.31
DANN	Benign	0.14
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs4939008; hg19: chr11-55690371;