rs3762055

Variant names:

• chr9-114328295-T-C
• rs3762055

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 0.0682 in 151,460 control chromosomes in the GnomAD database, including 75 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 0.068 (75 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.879

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0837 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: 0.0682 AC: 10326 AN: 151342 Hom.: 75 Cov.: 32

Gnomad AFR AF: 0.0862

Gnomad AMI AF: 0.0942

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.0594

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0212

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0725

Gnomad OTH AF: 0.0804

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

GnomAD4 genome AF: 0.0682 AC: 10324 AN: 151460 Hom.: 75 Cov.: 32 AF XY: 0.0656 AC XY: 4860 AN XY: 74056

Gnomad4 AFR AF: 0.0861

Gnomad4 AMR AF: 0.0694

Gnomad4 ASJ AF: 0.0594

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0193

Gnomad4 FIN AF: 0.0212

Gnomad4 NFE AF: 0.0725

Gnomad4 OTH AF: 0.0790

Alfa AF: 0.0713 Hom.: 4

Asia WGS AF: 0.0230 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.49
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3762055; hg19: chr9-117090575;