chr9-25737569-T-C

Variant names:

• chr9-25737569-T-C
• rs757099

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 0.386 in 152,076 control chromosomes in the GnomAD database, including 12,088 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 0.39 (12088 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 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: 0.387 AC: 58739 AN: 151958 Hom.: 12096 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.386 AC: 58733 AN: 152076 Hom.: 12088 Cov.: 33 AF XY: 0.387 AC XY: 28786 AN XY: 74350

African (AFR) AF: 0.240 AC: 9982 AN: 41514

American (AMR) AF: 0.397 AC: 6066 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1959 AN: 3468

East Asian (EAS) AF: 0.381 AC: 1967 AN: 5162

South Asian (SAS) AF: 0.503 AC: 2427 AN: 4824

European-Finnish (FIN) AF: 0.394 AC: 4162 AN: 10570

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30703 AN: 67938

Other (OTH) AF: 0.418 AC: 884 AN: 2114

Alfa AF: 0.434 Hom.: 58708

Bravo AF: 0.376

Asia WGS AF: 0.394 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.51
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs757099; hg19: chr9-25737567;