chr5-175445880-C-A

Variant names:

• chr5-175445880-C-A
• rs267410

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 0.369 in 151,496 control chromosomes in the GnomAD database, including 11,612 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 0.37 (11612 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 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: 0.369 AC: 55824 AN: 151376 Hom.: 11602 Cov.: 30

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.369 AC: 55853 AN: 151496 Hom.: 11612 Cov.: 30 AF XY: 0.371 AC XY: 27479 AN XY: 73992

African (AFR) AF: 0.170 AC: 7035 AN: 41290

American (AMR) AF: 0.436 AC: 6636 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1351 AN: 3466

East Asian (EAS) AF: 0.481 AC: 2433 AN: 5058

South Asian (SAS) AF: 0.313 AC: 1506 AN: 4806

European-Finnish (FIN) AF: 0.475 AC: 4993 AN: 10502

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30548 AN: 67840

Other (OTH) AF: 0.389 AC: 821 AN: 2110

Alfa AF: 0.260 Hom.: 740

Bravo AF: 0.357

Asia WGS AF: 0.392 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs267410; hg19: chr5-174872883; COSMIC: COSV67104362;