rs1490936

Variant names:

• chr11-107197261-C-A
• rs1490936

Your query was ambiguous. Multiple possible variants found:

• chr11-107197261-C-A
• chr11-107197261-C-G

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 0.602 in 151,892 control chromosomes in the GnomAD database, including 28,706 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 0.60 (28706 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 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: 0.602 AC: 91442 AN: 151774 Hom.: 28714 Cov.: 30

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.602 AC: 91445 AN: 151892 Hom.: 28706 Cov.: 30 AF XY: 0.599 AC XY: 44505 AN XY: 74248

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.605

Alfa AF: 0.667 Hom.: 43770

Bravo AF: 0.588

Asia WGS AF: 0.595 AC: 2067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.15
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1490936; hg19: chr11-107067987;