chr19-260970-A-T

Position:

• chr19-260970-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 0.519 in 151,956 control chromosomes in the GnomAD database, including 20,969 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 0.52 (20969 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 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: 0.519 AC: 78810 AN: 151840 Hom.: 20974 Cov.: 32

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.519 AC: 78826 AN: 151956 Hom.: 20969 Cov.: 32 AF XY: 0.515 AC XY: 38257 AN XY: 74266

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.519

Alfa AF: 0.541 Hom.: 2789

Bravo AF: 0.510

Asia WGS AF: 0.323 AC: 1127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.1
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8102615; hg19: chr19-260970;