19-7671913-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 0.437 in 152,046 control chromosomes in the GnomAD database, including 17,052 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 0.44 (17052 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.682 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: 0.438 AC: 66492 AN: 151928 Hom.: 17041 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.437 AC: 66513 AN: 152046 Hom.: 17052 Cov.: 32 AF XY: 0.444 AC XY: 33011 AN XY: 74314

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.482

Alfa AF: 0.348 Hom.: 1059

Bravo AF: 0.410

Asia WGS AF: 0.577 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.0
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1477341; hg19: chr19-7736799;