chr3-163935422-C-T

Variant names:

• chr3-163935422-C-T
• rs1150433

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 0.183 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.187 AC: 7767 AN: 41466

American (AMR) AF: 0.167 AC: 2551 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 747 AN: 3466

East Asian (EAS) AF: 0.0454 AC: 235 AN: 5174

South Asian (SAS) AF: 0.0773 AC: 373 AN: 4826

European-Finnish (FIN) AF: 0.147 AC: 1558 AN: 10572

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13985 AN: 67990

Other (OTH) AF: 0.178 AC: 376 AN: 2110

Alfa AF: 0.196 Hom.: 11323

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
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs1150433; hg19: chr3-163653210;