19-43782508-T-C

Variant names:

• chr19-43782508-T-C
• rs3760983

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 0.556 in 151,838 control chromosomes in the GnomAD database, including 23,967 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 0.56 (23967 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 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: 0.556 AC: 84295 AN: 151720 Hom.: 23939 Cov.: 31

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.556 AC: 84372 AN: 151838 Hom.: 23967 Cov.: 31 AF XY: 0.561 AC XY: 41608 AN XY: 74174

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.552

Alfa AF: 0.555 Hom.: 6351

Bravo AF: 0.564

Asia WGS AF: 0.604 AC: 2097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3760983; hg19: chr19-44286660;