rs267412

chr5-175448469-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;