rs267418

Variant names:

• chr5-175453642-G-C
• rs267418

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 0.366 in 152,072 control chromosomes in the GnomAD database, including 11,578 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 (11578 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 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: 0.366 AC: 55676 AN: 151952 Hom.: 11570 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.366 AC: 55704 AN: 152072 Hom.: 11578 Cov.: 32 AF XY: 0.369 AC XY: 27453 AN XY: 74334

African (AFR) AF: 0.165 AC: 6838 AN: 41502

American (AMR) AF: 0.434 AC: 6642 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1399 AN: 3466

East Asian (EAS) AF: 0.443 AC: 2291 AN: 5174

South Asian (SAS) AF: 0.307 AC: 1478 AN: 4816

European-Finnish (FIN) AF: 0.479 AC: 5054 AN: 10544

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30652 AN: 67970

Other (OTH) AF: 0.388 AC: 820 AN: 2112

Alfa AF: 0.403 Hom.: 1676

Bravo AF: 0.354

Asia WGS AF: 0.372 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.32
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs267418; hg19: chr5-174880645; COSMIC: COSV71841779;