rs10495970

Variant names:

• chr2-49264671-G-A
• rs10495970
• ENST00000634588.1:n.493-143531G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634588.1(ENSG00000282890):​n.493-143531G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 151,874 control chromosomes in the GnomAD database, including 5,102 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 0.26 (5102 hom., cov: 32)
• Consequence: ENSG00000282890 ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

Genes affected

ENSG00000282890 (HGNC:58158):

ENSG00000282998 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 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
ENSG00000282890	ENST00000634588.1	n.493-143531G>A		intron_variant	Intron 2 of 4	5
ENSG00000282998	ENST00000635306.1	n.408-46043C>T		intron_variant	Intron 3 of 6	5

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38748 AN: 151756 Hom.: 5098 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.255 AC: 38778 AN: 151874 Hom.: 5102 Cov.: 32 AF XY: 0.256 AC XY: 19012 AN XY: 74214

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.257

Alfa AF: 0.241 Hom.: 2104

Bravo AF: 0.250

Asia WGS AF: 0.280 AC: 974 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495970; hg19: chr2-49491810;