chr10-58466175-A-G

Variant names:

• chr10-58466175-A-G
• rs2114561
• ENST00000720299.1:n.532+17339A>G

Variant summary

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

The ENST00000720299.1(ENSG00000293977):​n.532+17339A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,078 control chromosomes in the GnomAD database, including 37,026 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 0.69 (37026 hom., cov: 32)
• Consequence: ENSG00000293977 ENST00000720299.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121
• Publications: 4 publications found

Genes affected

ENSG00000293977 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720299.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293977	ENST00000720299.1		n.532+17339A>G		intron	N/A
	ENSG00000293977	ENST00000720300.1		n.97+11340A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104736 AN: 151960 Hom.: 37013 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.689 AC: 104788 AN: 152078 Hom.: 37026 Cov.: 32 AF XY: 0.687 AC XY: 51101 AN XY: 74330

African (AFR) AF: 0.523 AC: 21693 AN: 41450

American (AMR) AF: 0.759 AC: 11608 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2400 AN: 3472

East Asian (EAS) AF: 0.749 AC: 3867 AN: 5166

South Asian (SAS) AF: 0.580 AC: 2795 AN: 4818

European-Finnish (FIN) AF: 0.730 AC: 7730 AN: 10584

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52381 AN: 67990

Other (OTH) AF: 0.676 AC: 1427 AN: 2110

Alfa AF: 0.746 Hom.: 54387

Bravo AF: 0.689

Asia WGS AF: 0.621 AC: 2160 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.77
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2114561; hg19: chr10-60225935;