ENST00000711606.1:n.616-2631T>C

Variant names:

• chr15-93209649-T-C
• rs1872052
• ENST00000711606.1:n.616-2631T>C

Variant summary

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

The ENST00000711606.1(ENSG00000257060):​n.616-2631T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 152,084 control chromosomes in the GnomAD database, including 15,733 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 0.44 (15733 hom., cov: 33)
• Consequence: ENSG00000257060 ENST00000711606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385
• Publications: 6 publications found

Genes affected

ENSG00000257060 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000711606.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257060	ENST00000711606.1		n.616-2631T>C		intron	N/A
	ENSG00000257060	ENST00000791023.1		n.313-19078T>C		intron	N/A
	ENSG00000257060	ENST00000791051.1		n.526-19078T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67657 AN: 151966 Hom.: 15729 Cov.: 33

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.445 AC: 67676 AN: 152084 Hom.: 15733 Cov.: 33 AF XY: 0.446 AC XY: 33160 AN XY: 74344

African (AFR) AF: 0.343 AC: 14241 AN: 41490

American (AMR) AF: 0.339 AC: 5186 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1495 AN: 3466

East Asian (EAS) AF: 0.558 AC: 2892 AN: 5180

South Asian (SAS) AF: 0.508 AC: 2450 AN: 4824

European-Finnish (FIN) AF: 0.530 AC: 5606 AN: 10574

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.504 AC: 34275 AN: 67962

Other (OTH) AF: 0.427 AC: 900 AN: 2110

Alfa AF: 0.474 Hom.: 55193

Bravo AF: 0.425

Asia WGS AF: 0.515 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	13
DANN	Benign	0.82
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs1872052; hg19: chr15-93752878;