rs4938544

Variant names:

• chr11-118794300-A-G
• rs4938544

Your query was ambiguous. Multiple possible variants found:

• chr11-118794300-A-G
• chr11-118794300-A-T

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 0.865 in 150,488 control chromosomes in the GnomAD database, including 56,489 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 0.86 (56489 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.45
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.22).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.865 AC: 130078 AN: 150404 Hom.: 56454 Cov.: 28

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.808

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.865 AC: 130151 AN: 150488 Hom.: 56489 Cov.: 28 AF XY: 0.866 AC XY: 63613 AN XY: 73482

African (AFR) AF: 0.801 AC: 32897 AN: 41054

American (AMR) AF: 0.900 AC: 13668 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.904 AC: 3131 AN: 3462

East Asian (EAS) AF: 0.999 AC: 5166 AN: 5170

South Asian (SAS) AF: 0.893 AC: 4274 AN: 4784

European-Finnish (FIN) AF: 0.895 AC: 8862 AN: 9902

Middle Eastern (MID) AF: 0.825 AC: 236 AN: 286

European-Non Finnish (NFE) AF: 0.876 AC: 59248 AN: 67658

Other (OTH) AF: 0.875 AC: 1822 AN: 2082

Alfa AF: 0.869 Hom.: 6721

Bravo AF: 0.862

Asia WGS AF: 0.935 AC: 3251 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	0.12
DANN	Benign	0.096
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs4938544; hg19: chr11-118665009;