rs7034647

Positions:

• chr9-108667644-A-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 0.127 in 151,574 control chromosomes in the GnomAD database, including 1,284 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 0.13 (1284 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.74

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 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: 0.127 AC: 19298 AN: 151456 Hom.: 1285 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0254

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.127 AC: 19292 AN: 151574 Hom.: 1284 Cov.: 31 AF XY: 0.129 AC XY: 9515 AN XY: 74034

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.0718

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.118

Alfa AF: 0.111 Hom.: 1511

Bravo AF: 0.125

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	10
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7034647; hg19: chr9-111429924; COSMIC: COSV60392121;