rs716004

Variant names:

• chr9-107345581-C-T
• rs716004

Variant summary

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

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0309 AC: 1281 AN: 41514

American (AMR) AF: 0.113 AC: 1735 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 451 AN: 3460

East Asian (EAS) AF: 0.0182 AC: 94 AN: 5170

South Asian (SAS) AF: 0.154 AC: 744 AN: 4818

European-Finnish (FIN) AF: 0.139 AC: 1470 AN: 10578

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11198 AN: 68002

Other (OTH) AF: 0.122 AC: 257 AN: 2112

Alfa AF: 0.154 Hom.: 3719

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
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs716004; hg19: chr9-110107862;