rs501371

Variant names:

• chr11-102877720-A-G
• rs501371

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 0.136 in 152,166 control chromosomes in the GnomAD database, including 2,446 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 0.14 (2446 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 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: 0.135 AC: 20602 AN: 152046 Hom.: 2438 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0847

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.0407

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0536

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.136 AC: 20624 AN: 152166 Hom.: 2446 Cov.: 32 AF XY: 0.133 AC XY: 9876 AN XY: 74388

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.0845

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0927

Gnomad4 FIN AF: 0.0407

Gnomad4 NFE AF: 0.0536

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0745 Hom.: 424

Bravo AF: 0.147

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs501371; hg19: chr11-102748450;