rs17586756

Variant names:

• chr2-118072882-C-T
• rs17586756
• ENST00000747789.1:n.231+14631G>A

Variant summary

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

The ENST00000747789.1(ENSG00000297418):​n.231+14631G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0362 in 152,292 control chromosomes in the GnomAD database, including 121 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 0.036 (121 hom., cov: 32)
• Consequence: ENSG00000297418 ENST00000747789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 2 publications found

Genes affected

ENSG00000297418 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0362 (5506/152292) while in subpopulation NFE AF = 0.05 (3399/68022). AF 95% confidence interval is 0.0486. There are 121 homozygotes in GnomAd4. There are 2644 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 121 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747789.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297418	ENST00000747789.1		n.231+14631G>A		intron	N/A
	ENSG00000297418	ENST00000747790.1		n.104+15369G>A		intron	N/A
	ENSG00000297418	ENST00000747791.1		n.331+1612G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0362 AC: 5510 AN: 152174 Hom.: 121 Cov.: 32

Gnomad AFR AF: 0.0172

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0440

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.0324

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0500

Gnomad OTH AF: 0.0483

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

GnomAD4 genome AF: 0.0362 AC: 5506 AN: 152292 Hom.: 121 Cov.: 32 AF XY: 0.0355 AC XY: 2644 AN XY: 74468

African (AFR) AF: 0.0172 AC: 716 AN: 41562

American (AMR) AF: 0.0439 AC: 671 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0424 AC: 147 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5186

South Asian (SAS) AF: 0.0122 AC: 59 AN: 4828

European-Finnish (FIN) AF: 0.0324 AC: 344 AN: 10616

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.0500 AC: 3399 AN: 68022

Other (OTH) AF: 0.0478 AC: 101 AN: 2112

Alfa AF: 0.0435 Hom.: 30

Bravo AF: 0.0367

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.4
DANN	Benign	0.80
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs17586756; hg19: chr2-118830458;