rs2816517

Variant names:

• chr8-5920479-C-A
• rs2816517
• ENST00000747096.1:n.267-20748G>T

Variant summary

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

The ENST00000747096.1(ENSG00000297321):​n.267-20748G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,916 control chromosomes in the GnomAD database, including 8,973 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 0.33 (8973 hom., cov: 32)
• Consequence: ENSG00000297321 ENST00000747096.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38
• Publications: 3 publications found

Genes affected

ENSG00000297321 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747096.1. 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
	ENSG00000297321	ENST00000747096.1		n.267-20748G>T		intron	N/A
	ENSG00000297321	ENST00000747097.1		n.169-20748G>T		intron	N/A
	ENSG00000297321	ENST00000747098.1		n.190-20748G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50581 AN: 151800 Hom.: 8960 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.333 AC: 50630 AN: 151916 Hom.: 8973 Cov.: 32 AF XY: 0.335 AC XY: 24894 AN XY: 74264

African (AFR) AF: 0.215 AC: 8939 AN: 41482

American (AMR) AF: 0.437 AC: 6657 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3468

East Asian (EAS) AF: 0.164 AC: 845 AN: 5142

South Asian (SAS) AF: 0.321 AC: 1547 AN: 4812

European-Finnish (FIN) AF: 0.394 AC: 4145 AN: 10528

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26329 AN: 67924

Other (OTH) AF: 0.353 AC: 746 AN: 2112

Alfa AF: 0.371 Hom.: 14140

Bravo AF: 0.333

Asia WGS AF: 0.290 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.22
DANN	Benign	0.13
PhyloP100		-2.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2816517;

hg19: chr8-5778001;