chr9-110609343-T-C

Variant names:

• chr9-110609343-T-C
• rs4295728

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 0.328 in 152,142 control chromosomes in the GnomAD database, including 9,634 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 0.33 (9634 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.572 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: 0.328 AC: 49841 AN: 152024 Hom.: 9624 Cov.: 33

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.328 AC: 49867 AN: 152142 Hom.: 9634 Cov.: 33 AF XY: 0.336 AC XY: 25006 AN XY: 74378

African (AFR) AF: 0.141 AC: 5840 AN: 41528

American (AMR) AF: 0.504 AC: 7698 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1248 AN: 3470

East Asian (EAS) AF: 0.590 AC: 3053 AN: 5176

South Asian (SAS) AF: 0.451 AC: 2173 AN: 4818

European-Finnish (FIN) AF: 0.415 AC: 4386 AN: 10568

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24453 AN: 67986

Other (OTH) AF: 0.355 AC: 746 AN: 2104

Alfa AF: 0.202 Hom.: 473

Bravo AF: 0.328

Asia WGS AF: 0.506 AC: 1743 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.014
DANN	Benign	0.46
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4295728; hg19: chr9-113371623;