rs9821642

Variant names:

• chr3-103626595-A-G
• rs9821642

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 0.375 in 150,894 control chromosomes in the GnomAD database, including 11,131 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 0.37 (11131 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 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: 0.374 AC: 56431 AN: 150776 Hom.: 11095 Cov.: 31

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.375 AC: 56529 AN: 150894 Hom.: 11131 Cov.: 31 AF XY: 0.384 AC XY: 28328 AN XY: 73704

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.391

Alfa AF: 0.319 Hom.: 13208

Bravo AF: 0.383

Asia WGS AF: 0.533 AC: 1844 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.7
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9821642; hg19: chr3-103345439;