rs379527

Variant names:

• chr19-6676431-C-A
• rs379527

Your query was ambiguous. Multiple possible variants found:

• chr19-6676431-C-A
• chr19-6676431-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;