ENST00000720299.1:n.533-18180T>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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378316	XR_007062374.1	n.518+17275T>C		intron_variant	Intron 3 of 3
LOC105378316	XR_945981.3	n.845+3473T>C		intron_variant	Intron 5 of 5
LOC105378316	XR_945982.3	n.811+3473T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293977	ENST00000720299.1	n.533-18180T>C		intron_variant	Intron 1 of 1
ENSG00000293977	ENST00000720300.1	n.98-18180T>C		intron_variant	Intron 1 of 1
ENSG00000293977	ENST00000720301.1	n.444+17275T>C		intron_variant	Intron 3 of 3
ENSG00000293977	ENST00000720302.1	n.581+17275T>C		intron_variant	Intron 1 of 1

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 v4.3

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;