rs265976

chr5-175435417-G-T

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 0.278 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.249

Alfa AF: 0.209 Hom.: 4903

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs265976; hg19: chr5-174862420;