rs716004

Positions:

• chr9-107345581-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.115 in 152,150 control chromosomes in the GnomAD database, including 1,287 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 0.11 (1287 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 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: 0.115 AC: 17442 AN: 152032 Hom.: 1288 Cov.: 31

Gnomad AFR AF: 0.0308

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.115 AC: 17446 AN: 152150 Hom.: 1287 Cov.: 31 AF XY: 0.114 AC XY: 8458 AN XY: 74372

Gnomad4 AFR AF: 0.0309

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.0182

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.122

Alfa AF: 0.160 Hom.: 2914

Bravo AF: 0.108

Asia WGS AF: 0.0840 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	14
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs716004; hg19: chr9-110107862;