rs10490122

Positions:

• chr2-48897855-G-A

Variant summary

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

The ENST00000634588.1(ENSG00000282890):​n.303-48361G>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 0.0271 in 152,204 control chromosomes in the GnomAD database, including 115 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 0.027 (115 hom., cov: 32)
• Consequence: ENST00000634588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000634588.1	n.303-48361G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0271 AC: 4114 AN: 152086 Hom.: 113 Cov.: 32

Gnomad AFR AF: 0.00766

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.0184

Gnomad ASJ AF: 0.00750

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.0946

Gnomad FIN AF: 0.0223

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0289

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0271 AC: 4120 AN: 152204 Hom.: 115 Cov.: 32 AF XY: 0.0285 AC XY: 2123 AN XY: 74426

Gnomad4 AFR AF: 0.00766

Gnomad4 AMR AF: 0.0184

Gnomad4 ASJ AF: 0.00750

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.0938

Gnomad4 FIN AF: 0.0223

Gnomad4 NFE AF: 0.0289

Gnomad4 OTH AF: 0.0369

Alfa AF: 0.0242 Hom.: 11

Bravo AF: 0.0260

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490122; hg19: chr2-49124994;