rs2421031

Variant names:

• chr10-122662592-T-C
• rs2421031
• ENST00000652317.1:n.47-1441T>C

Variant summary

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

The ENST00000652317.1(ENSG00000286114):​n.47-1441T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,788 control chromosomes in the GnomAD database, including 10,886 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 0.35 (10886 hom., cov: 31)
• Consequence: ENSG00000286114 ENST00000652317.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

ENSG00000286114 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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
ENSG00000286114	ENST00000652317.1	n.47-1441T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52583 AN: 151670 Hom.: 10872 Cov.: 31

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.347 AC: 52627 AN: 151788 Hom.: 10886 Cov.: 31 AF XY: 0.344 AC XY: 25476 AN XY: 74162

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.316

Alfa AF: 0.309 Hom.: 1050

Bravo AF: 0.362

Asia WGS AF: 0.275 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.32
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2421031; hg19: chr10-124422108;