rs11265501

Positions:

• chr1-160867138-G-A

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 0.318 in 151,990 control chromosomes in the GnomAD database, including 9,702 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 0.32 (9702 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48227 AN: 151872 Hom.: 9687 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.318 AC: 48293 AN: 151990 Hom.: 9702 Cov.: 32 AF XY: 0.318 AC XY: 23637 AN XY: 74288

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.287

Alfa AF: 0.271 Hom.: 868

Bravo AF: 0.329

Asia WGS AF: 0.422 AC: 1469 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	0.25
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11265501; hg19: chr1-160836928;