rs10497015

Variant names:

• chr2-147620501-T-C
• rs10497015
• ENST00000833959.1:n.263-42227A>G

Variant summary

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

The ENST00000833959.1(ENSG00000308424):​n.263-42227A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,662 control chromosomes in the GnomAD database, including 9,020 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 0.34 (9020 hom., cov: 30)
• Consequence: ENSG00000308424 ENST00000833959.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 2 publications found

Genes affected

ENSG00000308424 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308424	ENST00000833959.1	n.263-42227A>G		intron_variant	Intron 3 of 3
ENSG00000308424	ENST00000833960.1	n.451-42227A>G		intron_variant	Intron 2 of 2
ENSG00000308424	ENST00000833961.1	n.279-42227A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51433 AN: 151544 Hom.: 9024 Cov.: 30

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.339 AC: 51428 AN: 151662 Hom.: 9020 Cov.: 30 AF XY: 0.337 AC XY: 24950 AN XY: 74108

African (AFR) AF: 0.279 AC: 11526 AN: 41330

American (AMR) AF: 0.284 AC: 4324 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1577 AN: 3466

East Asian (EAS) AF: 0.231 AC: 1192 AN: 5166

South Asian (SAS) AF: 0.295 AC: 1422 AN: 4814

European-Finnish (FIN) AF: 0.347 AC: 3633 AN: 10482

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26475 AN: 67884

Other (OTH) AF: 0.372 AC: 782 AN: 2102

Alfa AF: 0.365 Hom.: 4289

Bravo AF: 0.334

Asia WGS AF: 0.249 AC: 865 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.3
DANN	Benign	0.63
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10497015; hg19: chr2-148378069;