19-6543331-T-C

Variant names:

• chr19-6543331-T-C
• rs348373

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 0.876 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
• Publications: 6 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 (NFE) allele frequency at 95% confidence interval = 0.89 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: 0.876 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

African (AFR) AF: 0.871 AC: 36118 AN: 41450

American (AMR) AF: 0.856 AC: 13030 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.862 AC: 2992 AN: 3472

East Asian (EAS) AF: 0.805 AC: 4154 AN: 5160

South Asian (SAS) AF: 0.816 AC: 3933 AN: 4822

European-Finnish (FIN) AF: 0.860 AC: 9072 AN: 10552

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.896 AC: 60909 AN: 67988

Other (OTH) AF: 0.869 AC: 1832 AN: 2108

Alfa AF: 0.887 Hom.: 201299

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs348373; hg19: chr19-6543342;