chr4-122587346-G-A

Variant names:

• chr4-122587346-G-A
• rs12642902

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 0.331 in 151,964 control chromosomes in the GnomAD database, including 8,626 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 0.33 (8626 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 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: 0.331 AC: 50333 AN: 151848 Hom.: 8621 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.331 AC: 50375 AN: 151964 Hom.: 8626 Cov.: 32 AF XY: 0.326 AC XY: 24200 AN XY: 74268

African (AFR) AF: 0.341 AC: 14142 AN: 41426

American (AMR) AF: 0.364 AC: 5562 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1178 AN: 3472

East Asian (EAS) AF: 0.457 AC: 2363 AN: 5168

South Asian (SAS) AF: 0.294 AC: 1415 AN: 4814

European-Finnish (FIN) AF: 0.198 AC: 2092 AN: 10562

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22509 AN: 67948

Other (OTH) AF: 0.324 AC: 684 AN: 2108

Alfa AF: 0.333 Hom.: 26872

Bravo AF: 0.346

Asia WGS AF: 0.364 AC: 1263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.5
DANN	Benign	0.78
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs12642902; hg19: chr4-123508501;