5-4966904-C-A

Variant names:

• chr5-4966904-C-A
• rs1947339

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 0.372 in 151,894 control chromosomes in the GnomAD database, including 10,726 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 (10726 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 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: 56413 AN: 151776 Hom.: 10714 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.372 AC: 56471 AN: 151894 Hom.: 10726 Cov.: 32 AF XY: 0.373 AC XY: 27662 AN XY: 74208

African (AFR) AF: 0.426 AC: 17659 AN: 41420

American (AMR) AF: 0.339 AC: 5174 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 996 AN: 3468

East Asian (EAS) AF: 0.360 AC: 1858 AN: 5166

South Asian (SAS) AF: 0.421 AC: 2023 AN: 4806

European-Finnish (FIN) AF: 0.367 AC: 3863 AN: 10522

Middle Eastern (MID) AF: 0.255 AC: 74 AN: 290

European-Non Finnish (NFE) AF: 0.353 AC: 23960 AN: 67942

Other (OTH) AF: 0.339 AC: 717 AN: 2114

Alfa AF: 0.268 Hom.: 839

Bravo AF: 0.372

Asia WGS AF: 0.400 AC: 1387 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	0.048
DANN	Benign	0.47
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs1947339; hg19: chr5-4967017;