chr3-196180782-T-C

Variant names:

• chr3-196180782-T-C
• rs4916483

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 0.126 in 152,168 control chromosomes in the GnomAD database, including 1,934 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 0.13 (1934 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 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: 0.126 AC: 19122 AN: 152052 Hom.: 1921 Cov.: 31

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.0822

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.126 AC: 19144 AN: 152168 Hom.: 1934 Cov.: 31 AF XY: 0.132 AC XY: 9784 AN XY: 74380

Gnomad4 AFR AF: 0.0298

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.0822

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.163

Alfa AF: 0.139 Hom.: 3651

Bravo AF: 0.130

Asia WGS AF: 0.395 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4916483; hg19: chr3-195907653;