19-7739434-A-T

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 0.714 in 151,942 control chromosomes in the GnomAD database, including 41,661 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 0.71 (41661 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 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: 0.714 AC: 108445 AN: 151824 Hom.: 41645 Cov.: 30

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.714 AC: 108492 AN: 151942 Hom.: 41661 Cov.: 30 AF XY: 0.716 AC XY: 53165 AN XY: 74246

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.878

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.758

Alfa AF: 0.771 Hom.: 5605

Bravo AF: 0.695

Asia WGS AF: 0.728 AC: 2532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.3
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8112310; hg19: chr19-7804320;