19-47786046-T-C

Variant names:

• chr19-47786046-T-C
• rs2042286

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 0.603 in 151,914 control chromosomes in the GnomAD database, including 27,785 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 0.60 (27785 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.706 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: 0.603 AC: 91551 AN: 151794 Hom.: 27745 Cov.: 31

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.603 AC: 91655 AN: 151914 Hom.: 27785 Cov.: 31 AF XY: 0.606 AC XY: 44963 AN XY: 74246

African (AFR) AF: 0.585 AC: 24259 AN: 41434

American (AMR) AF: 0.636 AC: 9680 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1817 AN: 3468

East Asian (EAS) AF: 0.648 AC: 3347 AN: 5166

South Asian (SAS) AF: 0.726 AC: 3496 AN: 4818

European-Finnish (FIN) AF: 0.578 AC: 6094 AN: 10546

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40971 AN: 67938

Other (OTH) AF: 0.568 AC: 1200 AN: 2114

Alfa AF: 0.605 Hom.: 109924

Bravo AF: 0.603

Asia WGS AF: 0.682 AC: 2373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.21
DANN	Benign	0.48
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs2042286; hg19: chr19-48289303; COSMIC: COSV72682679;