19-10960472-A-T

Position:

• chr19-10960472-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 0.37 in 152,052 control chromosomes in the GnomAD database, including 10,466 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 0.37 (10466 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56182 AN: 151934 Hom.: 10445 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.370 AC: 56250 AN: 152052 Hom.: 10466 Cov.: 33 AF XY: 0.369 AC XY: 27462 AN XY: 74332

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.369

Alfa AF: 0.369 Hom.: 1351

Bravo AF: 0.364

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.17
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11880865; hg19: chr19-11071148;