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:58939):

LOC105373703 (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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000799383.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000304068	ENST00000799383.1		n.877-30576T>C		intron	N/A
	ENSG00000304068	ENST00000799384.1		n.694-26440T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10497151;

hg19: chr2-156697096;