rs2421027

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

ENSG00000285955 (HGNC:58122):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0623 AC: 2585 AN: 41506

American (AMR) AF: 0.0942 AC: 1439 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 553 AN: 3470

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5186

South Asian (SAS) AF: 0.143 AC: 690 AN: 4824

European-Finnish (FIN) AF: 0.0658 AC: 689 AN: 10474

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.115 AC: 7786 AN: 67928

Other (OTH) AF: 0.103 AC: 217 AN: 2112

Alfa AF: 0.102 Hom.: 667

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
PhyloP100		-0.034

Splicing

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

Other links and lift over

dbSNP: rs2421027; hg19: chr10-124203648;