10-58451030-T-G

Variant names:

• chr10-58451030-T-G
• rs10509091
• ENST00000720299.1:n.532+2194T>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+2194T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,018 control chromosomes in the GnomAD database, including 31,618 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 0.61 (31618 hom., cov: 32)
• Consequence: ENSG00000293977 ENST00000720299.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 8 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.756 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293977	ENST00000720299.1		n.532+2194T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93159 AN: 151900 Hom.: 31615 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.613 AC: 93178 AN: 152018 Hom.: 31618 Cov.: 32 AF XY: 0.613 AC XY: 45500 AN XY: 74260

African (AFR) AF: 0.297 AC: 12303 AN: 41486

American (AMR) AF: 0.725 AC: 11075 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2392 AN: 3466

East Asian (EAS) AF: 0.661 AC: 3407 AN: 5158

South Asian (SAS) AF: 0.560 AC: 2698 AN: 4822

European-Finnish (FIN) AF: 0.699 AC: 7358 AN: 10530

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.761 AC: 51758 AN: 67972

Other (OTH) AF: 0.620 AC: 1310 AN: 2112

Alfa AF: 0.563 Hom.: 10777

Bravo AF: 0.606

Asia WGS AF: 0.559 AC: 1936 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.72
PhyloP100		0.10

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10509091;

hg19: chr10-60210790;