rs265976

Variant names:

• chr5-175435417-G-T
• rs265976

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.278 in 151,944 control chromosomes in the GnomAD database, including 7,178 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 0.28 (7178 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 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: 0.277 AC: 42130 AN: 151826 Hom.: 7161 Cov.: 31

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.278 AC: 42187 AN: 151944 Hom.: 7178 Cov.: 31 AF XY: 0.271 AC XY: 20110 AN XY: 74262

African (AFR) AF: 0.491 AC: 20340 AN: 41416

American (AMR) AF: 0.188 AC: 2874 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 531 AN: 3466

East Asian (EAS) AF: 0.183 AC: 944 AN: 5156

South Asian (SAS) AF: 0.182 AC: 875 AN: 4808

European-Finnish (FIN) AF: 0.208 AC: 2198 AN: 10578

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13672 AN: 67948

Other (OTH) AF: 0.249 AC: 526 AN: 2112

Alfa AF: 0.226 Hom.: 13478

Bravo AF: 0.286

Asia WGS AF: 0.223 AC: 778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.021
DANN	Benign	0.099
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs265976; hg19: chr5-174862420;