rs2816514

Variant names:

• chr8-5917813-C-A
• rs2816514
• ENST00000747096.1:n.267-18082G>T

Variant summary

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

The ENST00000747096.1(ENSG00000297321):​n.267-18082G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,094 control chromosomes in the GnomAD database, including 4,123 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 0.22 (4123 hom., cov: 32)
• Consequence: ENSG00000297321 ENST00000747096.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.324 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.267-18082G>T		intron	N/A
	ENSG00000297321	ENST00000747097.1		n.169-18082G>T		intron	N/A
	ENSG00000297321	ENST00000747098.1		n.190-18082G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33495 AN: 151976 Hom.: 4110 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.221 AC: 33537 AN: 152094 Hom.: 4123 Cov.: 32 AF XY: 0.224 AC XY: 16650 AN XY: 74350

African (AFR) AF: 0.122 AC: 5063 AN: 41522

American (AMR) AF: 0.332 AC: 5067 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 755 AN: 3466

East Asian (EAS) AF: 0.154 AC: 797 AN: 5168

South Asian (SAS) AF: 0.288 AC: 1389 AN: 4818

European-Finnish (FIN) AF: 0.245 AC: 2588 AN: 10576

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17044 AN: 67974

Other (OTH) AF: 0.234 AC: 494 AN: 2108

Alfa AF: 0.209 Hom.: 1687

Bravo AF: 0.221

Asia WGS AF: 0.257 AC: 895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.47
PhyloP100		0.096

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: rs2816514;

hg19: chr8-5775335;