rs4938544

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.900

Gnomad4 ASJ AF: 0.904

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.893

Gnomad4 FIN AF: 0.895

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.875

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4938544; hg19: chr11-118665009;