rs7853656

Positions:

• chr9-22144531-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 0.203 in 151,878 control chromosomes in the GnomAD database, including 3,517 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 0.20 (3517 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30718 AN: 151760 Hom.: 3509 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0792

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.203 AC: 30769 AN: 151878 Hom.: 3517 Cov.: 31 AF XY: 0.199 AC XY: 14813 AN XY: 74270

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.0792

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.211

Alfa AF: 0.191 Hom.: 2215

Bravo AF: 0.205

Asia WGS AF: 0.186 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
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: rs7853656; hg19: chr9-22144530; COSMIC: COSV69451115;