rs10495970

chr2-49264671-G-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, non coding transcript 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: ENST00000634588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634588.1	n.493-143531G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000635306.1	n.408-46043C>T		intron_variant, non_coding_transcript_variant		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;