9-108133073-C-T

Variant names:

• chr9-108133073-C-T
• rs676256
• XR_001746881.2:n.721-79779G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001746881.2(LOC105376214):​n.721-79779G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 152,056 control chromosomes in the GnomAD database, including 36,294 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 0.69 (36294 hom., cov: 32)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32
• Publications: 16 publications found

Genes affected

LOC105376214 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104263 AN: 151938 Hom.: 36236 Cov.: 32

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.686 AC: 104382 AN: 152056 Hom.: 36294 Cov.: 32 AF XY: 0.695 AC XY: 51637 AN XY: 74316

African (AFR) AF: 0.753 AC: 31253 AN: 41510

American (AMR) AF: 0.668 AC: 10207 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2208 AN: 3470

East Asian (EAS) AF: 0.957 AC: 4942 AN: 5166

South Asian (SAS) AF: 0.855 AC: 4129 AN: 4828

European-Finnish (FIN) AF: 0.659 AC: 6938 AN: 10536

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.625 AC: 42490 AN: 67968

Other (OTH) AF: 0.682 AC: 1438 AN: 2110

Alfa AF: 0.647 Hom.: 53768

Bravo AF: 0.688

Asia WGS AF: 0.893 AC: 3099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.018
DANN	Benign	0.71
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs676256; hg19: chr9-110895353; COSMIC: COSV60390074;