3-163935422-C-T

Position:

• chr3-163935422-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 0.183 in 152,084 control chromosomes in the GnomAD database, including 2,627 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 0.18 (2627 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 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: 0.183 AC: 27759 AN: 151964 Hom.: 2627 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0453

Gnomad SAS AF: 0.0773

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.183 AC: 27765 AN: 152084 Hom.: 2627 Cov.: 32 AF XY: 0.177 AC XY: 13181 AN XY: 74352

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.0454

Gnomad4 SAS AF: 0.0773

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.178

Alfa AF: 0.200 Hom.: 5694

Bravo AF: 0.186

Asia WGS AF: 0.0680 AC: 238 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1150433; hg19: chr3-163653210;