ENST00000759658.1:n.317-58821T>C

Variant names:

• chr6-79143023-T-C
• rs956550
• ENST00000759658.1:n.317-58821T>C

Variant summary

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

The ENST00000759658.1(ENSG00000286340):​n.317-58821T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,934 control chromosomes in the GnomAD database, including 5,331 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 0.26 (5331 hom., cov: 32)
• Consequence: ENSG00000286340 ENST00000759658.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 1 publications found

Genes affected

ENSG00000286340 (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 = 0.301 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000759658.1. 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
	ENSG00000286340	ENST00000759658.1		n.317-58821T>C		intron	N/A
	ENSG00000286340	ENST00000759659.1		n.179-37464T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38854 AN: 151816 Hom.: 5332 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.256 AC: 38865 AN: 151934 Hom.: 5331 Cov.: 32 AF XY: 0.255 AC XY: 18942 AN XY: 74264

African (AFR) AF: 0.166 AC: 6871 AN: 41484

American (AMR) AF: 0.286 AC: 4366 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 772 AN: 3468

East Asian (EAS) AF: 0.190 AC: 977 AN: 5144

South Asian (SAS) AF: 0.163 AC: 787 AN: 4820

European-Finnish (FIN) AF: 0.330 AC: 3488 AN: 10564

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20654 AN: 67902

Other (OTH) AF: 0.266 AC: 560 AN: 2108

Alfa AF: 0.282 Hom.: 1078

Bravo AF: 0.251

Asia WGS AF: 0.162 AC: 563 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.27
DANN	Benign	0.41
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs956550; hg19: chr6-79852740;