chr19-34165501-C-T

Position:

• chr19-34165501-C-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 0.34 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.321

Alfa AF: 0.337 Hom.: 6879

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs587259; hg19: chr19-34656406;