2-9119469-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105373415 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373415	XR_007086202.1	n.831+795A>G		intron_variant	Intron 2 of 2
LOC105373415	XR_922770.1	n.831+795A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.556

Alfa AF: 0.617 Hom.: 43450

Bravo AF: 0.494

Asia WGS AF: 0.706 AC: 2449 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9636252; hg19: chr2-9259598;