rs1321632

Variant names:

• chr3-197365786-C-T
• rs1321632

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;