rs2215496

Variant names:

• chr17-5743244-A-G
• rs2215496
• ENST00000783338.1:n.186+29426T>C

Your query was ambiguous. Multiple possible variants found:

• chr17-5743244-A-G
• chr17-5743244-A-T

Variant summary

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

The ENST00000783338.1(ENSG00000286356):​n.186+29426T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,584 control chromosomes in the GnomAD database, including 18,031 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 0.49 (18031 hom., cov: 31)
• Consequence: ENSG00000286356 ENST00000783338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 8 publications found

Genes affected

ENSG00000286356 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

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
ENSG00000286356	ENST00000783338.1	n.186+29426T>C		intron_variant	Intron 1 of 1
ENSG00000286356	ENST00000783339.1	n.174-23899T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73521 AN: 151464 Hom.: 18012 Cov.: 31

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.485 AC: 73591 AN: 151584 Hom.: 18031 Cov.: 31 AF XY: 0.483 AC XY: 35782 AN XY: 74036

African (AFR) AF: 0.510 AC: 21038 AN: 41220

American (AMR) AF: 0.530 AC: 8082 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1970 AN: 3462

East Asian (EAS) AF: 0.278 AC: 1434 AN: 5164

South Asian (SAS) AF: 0.439 AC: 2106 AN: 4792

European-Finnish (FIN) AF: 0.447 AC: 4704 AN: 10524

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32682 AN: 67870

Other (OTH) AF: 0.502 AC: 1060 AN: 2110

Alfa AF: 0.482 Hom.: 46290

Bravo AF: 0.490

Asia WGS AF: 0.385 AC: 1326 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.69
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs2215496; hg19: chr17-5646564;