chr19-17791525-T-C

Variant names:

• chr19-17791525-T-C
• rs265548

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 0.577 in 151,974 control chromosomes in the GnomAD database, including 26,302 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 0.58 (26302 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.994
• Publications: 20 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 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: 0.577 AC: 87562 AN: 151856 Hom.: 26254 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.577 AC: 87671 AN: 151974 Hom.: 26302 Cov.: 31 AF XY: 0.571 AC XY: 42408 AN XY: 74280

African (AFR) AF: 0.733 AC: 30401 AN: 41450

American (AMR) AF: 0.496 AC: 7564 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1694 AN: 3470

East Asian (EAS) AF: 0.256 AC: 1321 AN: 5170

South Asian (SAS) AF: 0.420 AC: 2025 AN: 4822

European-Finnish (FIN) AF: 0.568 AC: 6003 AN: 10572

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36989 AN: 67936

Other (OTH) AF: 0.543 AC: 1143 AN: 2106

Alfa AF: 0.550 Hom.: 77490

Bravo AF: 0.574

Asia WGS AF: 0.399 AC: 1391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.77
DANN	Benign	0.27
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs265548; hg19: chr19-17902334;