rs267412

Variant names:

• chr5-175448469-A-G
• rs267412

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.372 in 152,048 control chromosomes in the GnomAD database, including 11,866 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 (11866 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.18

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• 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: 56487 AN: 151928 Hom.: 11857 Cov.: 33

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.372 AC: 56517 AN: 152048 Hom.: 11866 Cov.: 33 AF XY: 0.374 AC XY: 27825 AN XY: 74306

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.391

Alfa AF: 0.393 Hom.: 2416

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	-0.38
CADD	Benign	17
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs267412; hg19: chr5-174875472; COSMIC: COSV67104369;