rs7856345

Variant names:

• chr9-21196491-T-A
• rs7856345

Your query was ambiguous. Multiple possible variants found:

• chr9-21196491-T-A
• chr9-21196491-T-G

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 0.206 in 151,880 control chromosomes in the GnomAD database, including 3,580 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 0.21 (3580 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 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: 0.206 AC: 31255 AN: 151762 Hom.: 3579 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.206 AC: 31287 AN: 151880 Hom.: 3580 Cov.: 32 AF XY: 0.206 AC XY: 15318 AN XY: 74222

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.201

Alfa AF: 0.196 Hom.: 360

Bravo AF: 0.214

Asia WGS AF: 0.250 AC: 871 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	2.6
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7856345; hg19: chr9-21196490;