chr19-6543331-T-C

Position:

• chr19-6543331-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 0.876 in 151,986 control chromosomes in the GnomAD database, including 58,411 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 0.88 (58411 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.876 AC: 133062 AN: 151870 Hom.: 58371 Cov.: 30

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.862

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.876 AC: 133158 AN: 151986 Hom.: 58411 Cov.: 30 AF XY: 0.872 AC XY: 64782 AN XY: 74288

Gnomad4 AFR AF: 0.871

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.862

Gnomad4 EAS AF: 0.805

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.896

Gnomad4 OTH AF: 0.869

Alfa AF: 0.888 Hom.: 81354

Bravo AF: 0.877

Asia WGS AF: 0.821 AC: 2854 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs348373; hg19: chr19-6543342;