rs2421027

Variant names:

• chr10-122444132-A-G
• rs2421027
• ENST00000650300.1:n.1853-7500T>C

Variant summary

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

The ENST00000650300.1(ENSG00000285955):​n.1853-7500T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0933 in 151,982 control chromosomes in the GnomAD database, including 792 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 0.093 (792 hom., cov: 32)
• Consequence: ENSG00000285955 ENST00000650300.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

Genes affected

ENSG00000285955 (HGNC:58122):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.134 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
ENSG00000285955	ENST00000650300.1	n.1853-7500T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0934 AC: 14190 AN: 151866 Hom.: 793 Cov.: 32

Gnomad AFR AF: 0.0624

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0944

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0658

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0933 AC: 14183 AN: 151982 Hom.: 792 Cov.: 32 AF XY: 0.0913 AC XY: 6783 AN XY: 74320

Gnomad4 AFR AF: 0.0623

Gnomad4 AMR AF: 0.0942

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.0658

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.103

Alfa AF: 0.110 Hom.: 460

Bravo AF: 0.0901

Asia WGS AF: 0.0810 AC: 277 AN: 3416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.9
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2421027; hg19: chr10-124203648;