chr19-7566778-T-C

Variant names:

• chr19-7566778-T-C
• rs479651

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 0.628 in 151,696 control chromosomes in the GnomAD database, including 31,688 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 0.63 (31688 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 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: 0.627 AC: 95084 AN: 151576 Hom.: 31630 Cov.: 30

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.628 AC: 95194 AN: 151696 Hom.: 31688 Cov.: 30 AF XY: 0.624 AC XY: 46257 AN XY: 74132

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.640

Alfa AF: 0.418 Hom.: 1026

Bravo AF: 0.637

Asia WGS AF: 0.606 AC: 2111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.36
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs479651; hg19: chr19-7631664;