rs7849862

chr9-21191685-G-Achr9-21191685-G-Cchr9-21191685-G-T

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 0.181 in 151,774 control chromosomes in the GnomAD database, including 2,705 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 0.18 (2705 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27380 AN: 151656 Hom.: 2704 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.181 AC: 27404 AN: 151774 Hom.: 2705 Cov.: 31 AF XY: 0.182 AC XY: 13523 AN XY: 74144

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.184

Alfa AF: 0.125 Hom.: 283

Bravo AF: 0.185

Asia WGS AF: 0.244 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.5
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7849862; hg19: chr9-21191684;