rs265974

Variant names:

• chr5-175434237-A-G
• rs265974

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 0.465 in 152,132 control chromosomes in the GnomAD database, including 19,239 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 0.47 (19239 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.754 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: 0.465 AC: 70719 AN: 152014 Hom.: 19206 Cov.: 33

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.465 AC: 70805 AN: 152132 Hom.: 19239 Cov.: 33 AF XY: 0.459 AC XY: 34142 AN XY: 74380

African (AFR) AF: 0.761 AC: 31608 AN: 41512

American (AMR) AF: 0.409 AC: 6252 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 938 AN: 3468

East Asian (EAS) AF: 0.466 AC: 2408 AN: 5164

South Asian (SAS) AF: 0.302 AC: 1458 AN: 4824

European-Finnish (FIN) AF: 0.334 AC: 3538 AN: 10578

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23320 AN: 67978

Other (OTH) AF: 0.437 AC: 923 AN: 2114

Alfa AF: 0.393 Hom.: 42211

Bravo AF: 0.490

Asia WGS AF: 0.401 AC: 1394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.5
DANN	Benign	0.75
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs265974; hg19: chr5-174861240;