rs10497151

Variant names:

• chr2-155840584-A-G
• rs10497151
• ENST00000799383.1:n.877-30576T>C

Variant summary

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

The ENST00000799383.1(ENSG00000304068):​n.877-30576T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0669 in 152,074 control chromosomes in the GnomAD database, including 425 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 0.067 (425 hom., cov: 32)
• Consequence: ENSG00000304068 ENST00000799383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• Publications: 2 publications found

Genes affected

ENSG00000304068 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373703	XR_001739749.2	n.1019+19T>C		intron_variant	Intron 5 of 7
LOC105373703	XR_001739750.2	n.1019+19T>C		intron_variant	Intron 5 of 5
LOC105373703	XR_001739751.2	n.1019+19T>C		intron_variant	Intron 5 of 6
LOC105373703	XR_007088689.1	n.635-26440T>C		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304068	ENST00000799383.1	n.877-30576T>C		intron_variant	Intron 6 of 8
ENSG00000304068	ENST00000799384.1	n.694-26440T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0670 AC: 10180 AN: 151956 Hom.: 426 Cov.: 32

Gnomad AFR AF: 0.0547

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0459

Gnomad ASJ AF: 0.0855

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.0785

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0851

Gnomad OTH AF: 0.0647

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

GnomAD4 genome AF: 0.0669 AC: 10178 AN: 152074 Hom.: 425 Cov.: 32 AF XY: 0.0654 AC XY: 4863 AN XY: 74366

African (AFR) AF: 0.0545 AC: 2264 AN: 41534

American (AMR) AF: 0.0457 AC: 697 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0855 AC: 296 AN: 3464

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5174

South Asian (SAS) AF: 0.0128 AC: 62 AN: 4826

European-Finnish (FIN) AF: 0.0785 AC: 832 AN: 10604

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0851 AC: 5779 AN: 67900

Other (OTH) AF: 0.0640 AC: 135 AN: 2110

Alfa AF: 0.0780 Hom.: 247

Bravo AF: 0.0644

Asia WGS AF: 0.0160 AC: 56 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	13
DANN	Benign	0.79
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10497151; hg19: chr2-156697096;