chr10-58484957-T-C

Variant names:

• chr10-58484957-T-C
• rs7096154
• ENST00000720299.1:n.533-18180T>C

Variant summary

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

The ENST00000720299.1(ENSG00000293977):​n.533-18180T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,866 control chromosomes in the GnomAD database, including 16,111 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 0.46 (16111 hom., cov: 30)
• Consequence: ENSG00000293977 ENST00000720299.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.588 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.533-18180T>C		intron	N/A
	ENSG00000293977	ENST00000720300.1		n.98-18180T>C		intron	N/A
	ENSG00000293977	ENST00000720301.1		n.444+17275T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69391 AN: 151748 Hom.: 16083 Cov.: 30

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.457 AC: 69464 AN: 151866 Hom.: 16111 Cov.: 30 AF XY: 0.464 AC XY: 34422 AN XY: 74236

African (AFR) AF: 0.520 AC: 21505 AN: 41374

American (AMR) AF: 0.472 AC: 7212 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1193 AN: 3462

East Asian (EAS) AF: 0.606 AC: 3124 AN: 5154

South Asian (SAS) AF: 0.606 AC: 2917 AN: 4812

European-Finnish (FIN) AF: 0.416 AC: 4391 AN: 10544

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27772 AN: 67932

Other (OTH) AF: 0.454 AC: 958 AN: 2108

Alfa AF: 0.430 Hom.: 6881

Bravo AF: 0.464

Asia WGS AF: 0.608 AC: 2114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.73
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs7096154; hg19: chr10-60244717;