rs1165640

Variant names:

• chr3-193820202-C-T
• rs1165640

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 0.873 in 152,194 control chromosomes in the GnomAD database, including 58,212 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 0.87 (58212 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.905 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: 0.873 AC: 132822 AN: 152076 Hom.: 58175 Cov.: 33

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.873 AC: 132914 AN: 152194 Hom.: 58212 Cov.: 33 AF XY: 0.874 AC XY: 65000 AN XY: 74404

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.863

Gnomad4 ASJ AF: 0.901

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.924

Gnomad4 NFE AF: 0.911

Gnomad4 OTH AF: 0.867

Alfa AF: 0.905 Hom.: 88879

Bravo AF: 0.863

Asia WGS AF: 0.816 AC: 2833 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.89
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1165640; hg19: chr3-193537991;