19-34165501-C-T

Variant names:

• chr19-34165501-C-T
• rs587259

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 0.34 in 151,942 control chromosomes in the GnomAD database, including 9,202 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 0.34 (9202 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 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: 0.340 AC: 51555 AN: 151824 Hom.: 9193 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.340 AC: 51607 AN: 151942 Hom.: 9202 Cov.: 31 AF XY: 0.335 AC XY: 24865 AN XY: 74282

African (AFR) AF: 0.368 AC: 15242 AN: 41382

American (AMR) AF: 0.257 AC: 3928 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1207 AN: 3472

East Asian (EAS) AF: 0.00271 AC: 14 AN: 5174

South Asian (SAS) AF: 0.251 AC: 1208 AN: 4822

European-Finnish (FIN) AF: 0.359 AC: 3793 AN: 10578

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25029 AN: 67940

Other (OTH) AF: 0.321 AC: 676 AN: 2106

Alfa AF: 0.339 Hom.: 11808

Bravo AF: 0.331

Asia WGS AF: 0.126 AC: 441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.35
DANN	Benign	0.76
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs587259; hg19: chr19-34656406;