chr9-25359871-C-T

Variant names:

• chr9-25359871-C-T
• rs7862611

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 0.26 in 151,742 control chromosomes in the GnomAD database, including 5,879 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 0.26 (5879 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 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: 0.260 AC: 39458 AN: 151624 Hom.: 5869 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.260 AC: 39498 AN: 151742 Hom.: 5879 Cov.: 32 AF XY: 0.262 AC XY: 19457 AN XY: 74138

African (AFR) AF: 0.402 AC: 16654 AN: 41406

American (AMR) AF: 0.190 AC: 2901 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 628 AN: 3462

East Asian (EAS) AF: 0.407 AC: 2101 AN: 5156

South Asian (SAS) AF: 0.230 AC: 1109 AN: 4816

European-Finnish (FIN) AF: 0.249 AC: 2622 AN: 10536

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12807 AN: 67824

Other (OTH) AF: 0.248 AC: 522 AN: 2106

Alfa AF: 0.209 Hom.: 11274

Bravo AF: 0.265

Asia WGS AF: 0.257 AC: 893 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.78
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs7862611; hg19: chr9-25359869;