rs4346460

Variant names:

• chr20-23588763-C-T
• rs4346460

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 0.237 in 151,902 control chromosomes in the GnomAD database, including 4,558 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 0.24 (4558 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 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: 0.237 AC: 36025 AN: 151784 Hom.: 4552 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.0914

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.237 AC: 36061 AN: 151902 Hom.: 4558 Cov.: 32 AF XY: 0.238 AC XY: 17640 AN XY: 74208

African (AFR) AF: 0.302 AC: 12517 AN: 41392

American (AMR) AF: 0.157 AC: 2400 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 688 AN: 3466

East Asian (EAS) AF: 0.114 AC: 588 AN: 5172

South Asian (SAS) AF: 0.307 AC: 1474 AN: 4804

European-Finnish (FIN) AF: 0.252 AC: 2661 AN: 10544

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15125 AN: 67934

Other (OTH) AF: 0.228 AC: 480 AN: 2106

Alfa AF: 0.243 Hom.: 3055

Bravo AF: 0.230

Asia WGS AF: 0.186 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.023
DANN	Benign	0.31
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4346460; hg19: chr20-23569400; COSMIC: COSV71316647;