chr9-26714616-T-C

Variant names:

• chr9-26714616-T-C
• rs2060409

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 0.285 in 151,966 control chromosomes in the GnomAD database, including 6,472 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 0.29 (6472 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.332 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: 0.285 AC: 43341 AN: 151846 Hom.: 6463 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.285 AC: 43363 AN: 151966 Hom.: 6472 Cov.: 32 AF XY: 0.289 AC XY: 21481 AN XY: 74262

African (AFR) AF: 0.204 AC: 8471 AN: 41454

American (AMR) AF: 0.261 AC: 3982 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1125 AN: 3468

East Asian (EAS) AF: 0.281 AC: 1447 AN: 5158

South Asian (SAS) AF: 0.346 AC: 1667 AN: 4816

European-Finnish (FIN) AF: 0.369 AC: 3884 AN: 10528

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21726 AN: 67960

Other (OTH) AF: 0.316 AC: 667 AN: 2110

Alfa AF: 0.308 Hom.: 12321

Bravo AF: 0.274

Asia WGS AF: 0.297 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.70
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs2060409; hg19: chr9-26714614;