rs346416

Variant names:

• chr5-63246067-C-A
• rs346416

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 0.539 in 151,918 control chromosomes in the GnomAD database, including 24,605 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 0.54 (24605 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 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: 0.539 AC: 81770 AN: 151800 Hom.: 24569 Cov.: 32

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.539 AC: 81842 AN: 151918 Hom.: 24605 Cov.: 32 AF XY: 0.529 AC XY: 39306 AN XY: 74264

African (AFR) AF: 0.815 AC: 33838 AN: 41496

American (AMR) AF: 0.365 AC: 5558 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1523 AN: 3464

East Asian (EAS) AF: 0.275 AC: 1417 AN: 5158

South Asian (SAS) AF: 0.433 AC: 2089 AN: 4826

European-Finnish (FIN) AF: 0.398 AC: 4207 AN: 10560

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.462 AC: 31359 AN: 67860

Other (OTH) AF: 0.490 AC: 1031 AN: 2106

Alfa AF: 0.478 Hom.: 80060

Bravo AF: 0.546

Asia WGS AF: 0.352 AC: 1225 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.056
DANN	Benign	0.25
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs346416; hg19: chr5-62541894; COSMIC: COSV60145233;