rs266001

Variant names:

• chr5-175426567-G-A
• rs266001

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 0.14 in 152,080 control chromosomes in the GnomAD database, including 1,704 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 (1704 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 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: 0.140 AC: 21298 AN: 151962 Hom.: 1700 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.0899

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.140 AC: 21324 AN: 152080 Hom.: 1704 Cov.: 32 AF XY: 0.139 AC XY: 10354 AN XY: 74378

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.0897

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.124

Alfa AF: 0.129 Hom.: 464

Bravo AF: 0.143

Asia WGS AF: 0.118 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	10
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs266001; hg19: chr5-174853570; COSMIC: COSV60236591;