11-103487363-A-G

Variant names:

• chr11-103487363-A-G
• rs10895437

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 0.589 in 151,894 control chromosomes in the GnomAD database, including 28,616 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 0.59 (28616 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 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: 0.590 AC: 89487 AN: 151776 Hom.: 28616 Cov.: 30

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.589 AC: 89503 AN: 151894 Hom.: 28616 Cov.: 30 AF XY: 0.593 AC XY: 43980 AN XY: 74214

African (AFR) AF: 0.313 AC: 12972 AN: 41444

American (AMR) AF: 0.672 AC: 10238 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2446 AN: 3466

East Asian (EAS) AF: 0.724 AC: 3704 AN: 5114

South Asian (SAS) AF: 0.670 AC: 3225 AN: 4814

European-Finnish (FIN) AF: 0.686 AC: 7243 AN: 10552

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47564 AN: 67958

Other (OTH) AF: 0.622 AC: 1310 AN: 2106

Alfa AF: 0.569 Hom.: 3102

Bravo AF: 0.579

Asia WGS AF: 0.668 AC: 2321 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	0.18
DANN	Benign	0.30
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10895437; hg19: chr11-103358091;