ENST00000760372.1:n.235+20060A>T

Variant names:

• chr3-86737587-A-T
• rs10511060
• ENST00000760372.1:n.235+20060A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000760372.1(ENSG00000299083):​n.235+20060A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0235 in 152,288 control chromosomes in the GnomAD database, including 56 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 0.023 (56 hom., cov: 33)
• Consequence: ENSG00000299083 ENST00000760372.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.925
• Publications: 0 publications found

Genes affected

ENSG00000299083 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0235 (3578/152288) while in subpopulation NFE AF = 0.0362 (2464/67978). AF 95% confidence interval is 0.0351. There are 56 homozygotes in GnomAd4. There are 1753 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 56 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299083	ENST00000760372.1	n.235+20060A>T		intron_variant	Intron 2 of 3
ENSG00000299083	ENST00000760373.1	n.*238A>T		downstream_gene_variant
ENSG00000299083	ENST00000760374.1	n.*233A>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0235 AC: 3581 AN: 152170 Hom.: 56 Cov.: 33

Gnomad AFR AF: 0.00593

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0174

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.00827

Gnomad FIN AF: 0.0435

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0363

Gnomad OTH AF: 0.0120

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

GnomAD4 genome AF: 0.0235 AC: 3578 AN: 152288 Hom.: 56 Cov.: 33 AF XY: 0.0235 AC XY: 1753 AN XY: 74474

African (AFR) AF: 0.00589 AC: 245 AN: 41590

American (AMR) AF: 0.0173 AC: 265 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3466

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.00827 AC: 40 AN: 4834

European-Finnish (FIN) AF: 0.0435 AC: 462 AN: 10622

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0362 AC: 2464 AN: 67978

Other (OTH) AF: 0.0123 AC: 26 AN: 2114

Alfa AF: 0.0308 Hom.: 8

Bravo AF: 0.0206

Asia WGS AF: 0.00549 AC: 19 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.32
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs10511060; hg19: chr3-86786737;