rs376465

Variant names:

• chr19-22158230-T-C
• rs376465

Your query was ambiguous. Multiple possible variants found:

• chr19-22158230-T-C
• chr19-22158230-T-G

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 0.451 in 151,730 control chromosomes in the GnomAD database, including 16,763 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 0.45 (16763 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 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: 0.451 AC: 68376 AN: 151612 Hom.: 16727 Cov.: 31

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.451 AC: 68467 AN: 151730 Hom.: 16763 Cov.: 31 AF XY: 0.450 AC XY: 33342 AN XY: 74110

African (AFR) AF: 0.650 AC: 26864 AN: 41308

American (AMR) AF: 0.428 AC: 6529 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1512 AN: 3464

East Asian (EAS) AF: 0.358 AC: 1848 AN: 5158

South Asian (SAS) AF: 0.424 AC: 2042 AN: 4818

European-Finnish (FIN) AF: 0.344 AC: 3619 AN: 10510

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24677 AN: 67910

Other (OTH) AF: 0.420 AC: 885 AN: 2106

Alfa AF: 0.420 Hom.: 1741

Bravo AF: 0.463

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs376465; hg19: chr19-22341032;