chr19-260970-A-T

Variant names:

• chr19-260970-A-T
• rs8102615

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.569 AC: 23571 AN: 41450

American (AMR) AF: 0.460 AC: 7020 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1989 AN: 3472

East Asian (EAS) AF: 0.138 AC: 714 AN: 5170

South Asian (SAS) AF: 0.418 AC: 2015 AN: 4822

European-Finnish (FIN) AF: 0.601 AC: 6344 AN: 10562

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.521 AC: 35381 AN: 67918

Other (OTH) AF: 0.519 AC: 1095 AN: 2110

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

Other links and lift over

dbSNP: rs8102615; hg19: chr19-260970;