9-117525430-G-T

Variant names:

• chr9-117525430-G-T
• rs2771051

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 0.594 in 151,986 control chromosomes in the GnomAD database, including 27,516 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 0.59 (27516 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 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: 0.594 AC: 90216 AN: 151870 Hom.: 27490 Cov.: 32

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.594 AC: 90283 AN: 151986 Hom.: 27516 Cov.: 32 AF XY: 0.591 AC XY: 43874 AN XY: 74290

African (AFR) AF: 0.603 AC: 24979 AN: 41446

American (AMR) AF: 0.441 AC: 6726 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1983 AN: 3472

East Asian (EAS) AF: 0.242 AC: 1247 AN: 5150

South Asian (SAS) AF: 0.475 AC: 2285 AN: 4812

European-Finnish (FIN) AF: 0.707 AC: 7482 AN: 10584

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43524 AN: 67944

Other (OTH) AF: 0.567 AC: 1199 AN: 2114

Alfa AF: 0.608 Hom.: 52375

Bravo AF: 0.569

Asia WGS AF: 0.387 AC: 1351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.4
DANN	Benign	0.77
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs2771051; hg19: chr9-120287708;