rs7034647

Variant names:

• chr9-108667644-A-G
• rs7034647

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.150 AC: 6186 AN: 41368

American (AMR) AF: 0.144 AC: 2190 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0718 AC: 249 AN: 3466

East Asian (EAS) AF: 0.141 AC: 730 AN: 5160

South Asian (SAS) AF: 0.155 AC: 742 AN: 4780

European-Finnish (FIN) AF: 0.141 AC: 1480 AN: 10498

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 290

European-Non Finnish (NFE) AF: 0.109 AC: 7411 AN: 67760

Other (OTH) AF: 0.118 AC: 249 AN: 2102

Alfa AF: 0.111 Hom.: 1951

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
PhyloP100		1.7

Splicing

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

Other links and lift over

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