2-9119469-T-C

Variant names:

• chr2-9119469-T-C
• rs9636252
• XR_007086202.1:n.831+795A>G

Variant summary

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

The XR_922770.1(LOC105373415):​n.831+795A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,720 control chromosomes in the GnomAD database, including 23,335 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 0.51 (23335 hom., cov: 31)
• Consequence: LOC105373415 XR_922770.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495
• Publications: 7 publications found

Genes affected

LOC105373415 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 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: 0.514 AC: 77938 AN: 151614 Hom.: 23332 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.514 AC: 77936 AN: 151720 Hom.: 23335 Cov.: 31 AF XY: 0.517 AC XY: 38335 AN XY: 74124

African (AFR) AF: 0.186 AC: 7692 AN: 41384

American (AMR) AF: 0.585 AC: 8924 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2160 AN: 3470

East Asian (EAS) AF: 0.837 AC: 4336 AN: 5180

South Asian (SAS) AF: 0.661 AC: 3178 AN: 4810

European-Finnish (FIN) AF: 0.638 AC: 6639 AN: 10412

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.634 AC: 43083 AN: 67916

Other (OTH) AF: 0.556 AC: 1171 AN: 2106

Alfa AF: 0.581 Hom.: 63284

Bravo AF: 0.494

Asia WGS AF: 0.706 AC: 2449 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.54
DANN	Benign	0.68
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs9636252; hg19: chr2-9259598;