rs2042286

Positions:

• chr19-47786046-T-C

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 0.603 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.568

Alfa AF: 0.603 Hom.: 44586

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

Splicing

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

Publications

LitVar

Other links and lift over

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