chr3-187613802-C-T

Position:

• chr3-187613802-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 0.231 in 140,802 control chromosomes in the GnomAD database, including 4,029 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 0.23 (4029 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.231 AC: 32441 AN: 140702 Hom.: 4015 Cov.: 24

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.231 AC: 32474 AN: 140802 Hom.: 4029 Cov.: 24 AF XY: 0.241 AC XY: 16324 AN XY: 67674

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.221

Alfa AF: 0.196 Hom.: 3723

Bravo AF: 0.225

Asia WGS AF: 0.345 AC: 1199 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7635068; hg19: chr3-187331590;