3-197365786-C-T

Position:

• chr3-197365786-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 0.128 in 152,134 control chromosomes in the GnomAD database, including 1,761 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 (1761 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 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: 0.128 AC: 19497 AN: 152016 Hom.: 1758 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0928

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.0526

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0600

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.0762

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.128 AC: 19522 AN: 152134 Hom.: 1761 Cov.: 32 AF XY: 0.127 AC XY: 9422 AN XY: 74392

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.0927

Gnomad4 ASJ AF: 0.0559

Gnomad4 EAS AF: 0.0526

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0600

Gnomad4 NFE AF: 0.0763

Gnomad4 OTH AF: 0.121

Alfa AF: 0.0844 Hom.: 1146

Bravo AF: 0.134

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	13
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1321632; hg19: chr3-197092657;