rs7032940

Positions:

• chr9-110183125-G-A

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 0.204 in 152,130 control chromosomes in the GnomAD database, including 3,287 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 (3287 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.609

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.231 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: 0.204 AC: 31083 AN: 152012 Hom.: 3285 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.204 AC: 31095 AN: 152130 Hom.: 3287 Cov.: 32 AF XY: 0.200 AC XY: 14860 AN XY: 74382

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.224

Alfa AF: 0.234 Hom.: 6985

Bravo AF: 0.203

Asia WGS AF: 0.212 AC: 735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7032940; hg19: chr9-112945405;