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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378316	XR_007062374.1	n.95+14824T>G		intron_variant	Intron 1 of 3
LOC105378316	XR_945981.3	n.360+15373T>G		intron_variant	Intron 2 of 5
LOC105378316	XR_945982.3	n.360+15373T>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293977	ENST00000720299.1	n.532+2194T>G		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs10509091; hg19: chr10-60210790;