rs2279420

Variant names:

• chr10-60022189-A-G
• rs2279420
• ENST00000830353.1:n.83-28364A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000830353.1(ENSG00000232682):​n.83-28364A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0881 in 152,302 control chromosomes in the GnomAD database, including 683 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 0.088 (683 hom., cov: 33)
• Consequence: ENSG00000232682 ENST00000830353.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 5 publications found

Genes affected

ENSG00000232682 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.105 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
ENSG00000232682	ENST00000830353.1	n.83-28364A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0881 AC: 13412 AN: 152184 Hom.: 683 Cov.: 33

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.0427

Gnomad EAS AF: 0.0751

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0881 AC: 13413 AN: 152302 Hom.: 683 Cov.: 33 AF XY: 0.0904 AC XY: 6729 AN XY: 74462

African (AFR) AF: 0.0512 AC: 2131 AN: 41584

American (AMR) AF: 0.0737 AC: 1128 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0427 AC: 148 AN: 3470

East Asian (EAS) AF: 0.0756 AC: 392 AN: 5184

South Asian (SAS) AF: 0.113 AC: 543 AN: 4822

European-Finnish (FIN) AF: 0.145 AC: 1534 AN: 10604

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7206 AN: 68016

Other (OTH) AF: 0.0784 AC: 166 AN: 2116

Alfa AF: 0.0967 Hom.: 1238

Bravo AF: 0.0791

Asia WGS AF: 0.0870 AC: 306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.69
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2279420; hg19: chr10-61781947;