rs266001

Positions:

• chr5-175426567-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 0.14 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;