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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377795	XR_001745765.1	n.308-18082G>T		intron_variant	Intron 3 of 5
LOC105377795	XR_001745766.1	n.406-18082G>T		intron_variant	Intron 3 of 5
LOC105377795	XR_001745767.1	n.216-18082G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297321	ENST00000747096.1	n.267-18082G>T		intron_variant	Intron 3 of 5
ENSG00000297321	ENST00000747097.1	n.169-18082G>T		intron_variant	Intron 2 of 4
ENSG00000297321	ENST00000747098.1	n.190-18082G>T		intron_variant	Intron 2 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs2816514; hg19: chr8-5775335;