rs9820695

Variant names:

• chr3-103612639-G-A
• rs9820695

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 0.426 in 152,004 control chromosomes in the GnomAD database, including 15,447 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 0.43 (15447 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 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: 0.425 AC: 64596 AN: 151886 Hom.: 15395 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.426 AC: 64715 AN: 152004 Hom.: 15447 Cov.: 32 AF XY: 0.434 AC XY: 32217 AN XY: 74296

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.437

Alfa AF: 0.330 Hom.: 10704

Bravo AF: 0.441

Asia WGS AF: 0.544 AC: 1890 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.1
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9820695; hg19: chr3-103331483;