rs10512296

Variant names:

• chr9-102231390-T-C
• rs10512296
• ENST00000737266.1:n.95-15367T>C

Variant summary

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

The ENST00000737266.1(ENSG00000296202):​n.95-15367T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0508 in 152,264 control chromosomes in the GnomAD database, including 270 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 0.051 (270 hom., cov: 32)
• Consequence: ENSG00000296202 ENST00000737266.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 1 publications found

Genes affected

ENSG00000296202 (HGNC:):

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 = 0.0708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376188	XR_930188.3	n.262-1534T>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296202	ENST00000737266.1	n.95-15367T>C		intron_variant	Intron 1 of 2
ENSG00000296202	ENST00000737267.1	n.95-1534T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0508 AC: 7724 AN: 152146 Hom.: 268 Cov.: 32

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0613

Gnomad ASJ AF: 0.0384

Gnomad EAS AF: 0.0770

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0648

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0508 AC: 7729 AN: 152264 Hom.: 270 Cov.: 32 AF XY: 0.0511 AC XY: 3805 AN XY: 74456

African (AFR) AF: 0.0136 AC: 567 AN: 41568

American (AMR) AF: 0.0617 AC: 943 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0384 AC: 133 AN: 3468

East Asian (EAS) AF: 0.0770 AC: 399 AN: 5180

South Asian (SAS) AF: 0.0213 AC: 103 AN: 4830

European-Finnish (FIN) AF: 0.100 AC: 1060 AN: 10604

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0648 AC: 4409 AN: 68000

Other (OTH) AF: 0.0369 AC: 78 AN: 2114

Alfa AF: 0.0558 Hom.: 197

Bravo AF: 0.0478

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.71
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs10512296; hg19: chr9-104993672;