chr19-29805946-T-C

Variant names:

• chr19-29805946-T-C
• rs8102137

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 0.235 in 152,214 control chromosomes in the GnomAD database, including 5,181 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 0.24 (5181 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.900
• Publications: 71 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 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: 0.236 AC: 35845 AN: 152096 Hom.: 5180 Cov.: 33

Gnomad AFR AF: 0.0750

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.235 AC: 35842 AN: 152214 Hom.: 5181 Cov.: 33 AF XY: 0.233 AC XY: 17345 AN XY: 74394

African (AFR) AF: 0.0749 AC: 3113 AN: 41550

American (AMR) AF: 0.196 AC: 2996 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3472

East Asian (EAS) AF: 0.101 AC: 524 AN: 5180

South Asian (SAS) AF: 0.209 AC: 1007 AN: 4826

European-Finnish (FIN) AF: 0.364 AC: 3848 AN: 10582

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22291 AN: 67984

Other (OTH) AF: 0.241 AC: 510 AN: 2114

Alfa AF: 0.293 Hom.: 32652

Bravo AF: 0.216

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.92
DANN	Benign	0.46
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs8102137; hg19: chr19-30296853;