9-5260079-C-T

Variant names:

• chr9-5260079-C-T
• rs1830610

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 0.379 in 151,960 control chromosomes in the GnomAD database, including 12,678 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 0.38 (12678 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.11
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57501 AN: 151842 Hom.: 12648 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.379 AC: 57590 AN: 151960 Hom.: 12678 Cov.: 32 AF XY: 0.379 AC XY: 28164 AN XY: 74260

African (AFR) AF: 0.613 AC: 25405 AN: 41434

American (AMR) AF: 0.342 AC: 5223 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 860 AN: 3468

East Asian (EAS) AF: 0.243 AC: 1255 AN: 5170

South Asian (SAS) AF: 0.300 AC: 1450 AN: 4830

European-Finnish (FIN) AF: 0.350 AC: 3692 AN: 10534

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18614 AN: 67940

Other (OTH) AF: 0.352 AC: 745 AN: 2114

Alfa AF: 0.278 Hom.: 2146

Bravo AF: 0.384

Asia WGS AF: 0.303 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.25
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs1830610; hg19: chr9-5260079; COSMIC: COSV60323817;