rs8102137

chr19-29805946-T-C

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 0.235 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0749

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.241

Alfa AF: 0.307 Hom.: 17131

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8102137; hg19: chr19-30296853;