rs9820695

Positions:

• chr3-103612639-G-A

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.103612639G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;