rs379527

chr19-6676431-C-Achr19-6676431-C-G

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 0.728 in 152,008 control chromosomes in the GnomAD database, including 40,694 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 0.73 (40694 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.823

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 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: 0.728 AC: 110535 AN: 151890 Hom.: 40651 Cov.: 31

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.728 AC: 110634 AN: 152008 Hom.: 40694 Cov.: 31 AF XY: 0.724 AC XY: 53762 AN XY: 74270

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.738

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.713

Alfa AF: 0.695 Hom.: 49144

Bravo AF: 0.735

Asia WGS AF: 0.720 AC: 2506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.089
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs379527; hg19: chr19-6676442;