rs412658

Variant names:

• chr19-22176638-C-T
• rs412658

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.424 in 151,904 control chromosomes in the GnomAD database, including 14,469 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 0.42 (14469 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 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: 0.424 AC: 64357 AN: 151786 Hom.: 14452 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.424 AC: 64416 AN: 151904 Hom.: 14469 Cov.: 32 AF XY: 0.424 AC XY: 31448 AN XY: 74230

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.394

Alfa AF: 0.284 Hom.: 820

Bravo AF: 0.432

Asia WGS AF: 0.374 AC: 1298 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.9
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs412658; hg19: chr19-22359440;