rs267413

Variant names:

• chr5-175448605-A-T
• rs267413

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 0.371 in 152,142 control chromosomes in the GnomAD database, including 11,865 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 (11865 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.696
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 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: 0.372 AC: 56479 AN: 152022 Hom.: 11856 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.371 AC: 56509 AN: 152142 Hom.: 11865 Cov.: 33 AF XY: 0.374 AC XY: 27834 AN XY: 74368

African (AFR) AF: 0.171 AC: 7098 AN: 41522

American (AMR) AF: 0.439 AC: 6714 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1406 AN: 3470

East Asian (EAS) AF: 0.447 AC: 2314 AN: 5180

South Asian (SAS) AF: 0.313 AC: 1509 AN: 4826

European-Finnish (FIN) AF: 0.478 AC: 5050 AN: 10572

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

European-Non Finnish (NFE) AF: 0.457 AC: 31063 AN: 67976

Other (OTH) AF: 0.390 AC: 824 AN: 2112

Alfa AF: 0.408 Hom.: 1714

Bravo AF: 0.360

Asia WGS AF: 0.376 AC: 1303 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.9
DANN	Benign	0.63
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs267413; hg19: chr5-174875608; COSMIC: COSV67104371;