11-5201149-G-A

Variant names:

• chr11-5201149-G-A
• rs7937649

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 0.71 in 151,958 control chromosomes in the GnomAD database, including 39,711 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 0.71 (39711 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.821 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: 0.710 AC: 107816 AN: 151840 Hom.: 39700 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.710 AC: 107868 AN: 151958 Hom.: 39711 Cov.: 32 AF XY: 0.705 AC XY: 52366 AN XY: 74286

African (AFR) AF: 0.528 AC: 21855 AN: 41358

American (AMR) AF: 0.679 AC: 10369 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2982 AN: 3470

East Asian (EAS) AF: 0.504 AC: 2602 AN: 5162

South Asian (SAS) AF: 0.614 AC: 2960 AN: 4818

European-Finnish (FIN) AF: 0.776 AC: 8198 AN: 10562

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56220 AN: 67992

Other (OTH) AF: 0.747 AC: 1578 AN: 2112

Alfa AF: 0.675 Hom.: 9654

Bravo AF: 0.694

Asia WGS AF: 0.555 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.78
DANN	Benign	0.69
PhyloP100		-1.2
PromoterAI		-0.020	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7937649; hg19: chr11-5222379;