rs2567768

Variant names:

• chr8-97290923-G-A
• rs2567768
• ENST00000815218.1:n.203-2780C>T

Variant summary

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

The NR_125390.1(LOC101927066):​n.471+128147C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,156 control chromosomes in the GnomAD database, including 2,198 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 0.14 (2198 hom., cov: 33)
• Consequence: LOC101927066 NR_125390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 0 publications found

Genes affected

ENSG00000306089 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_125390.1. 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
	LOC101927066	NR_125390.1		n.471+128147C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306089	ENST00000815218.1		n.203-2780C>T		intron	N/A
	ENSG00000306089	ENST00000815219.1		n.118-129C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21513 AN: 152038 Hom.: 2201 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0652

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0751

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.141 AC: 21516 AN: 152156 Hom.: 2198 Cov.: 33 AF XY: 0.140 AC XY: 10413 AN XY: 74384

African (AFR) AF: 0.291 AC: 12050 AN: 41470

American (AMR) AF: 0.121 AC: 1852 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0617 AC: 214 AN: 3470

East Asian (EAS) AF: 0.120 AC: 624 AN: 5182

South Asian (SAS) AF: 0.150 AC: 725 AN: 4820

European-Finnish (FIN) AF: 0.0652 AC: 691 AN: 10596

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0751 AC: 5107 AN: 68004

Other (OTH) AF: 0.105 AC: 221 AN: 2112

Alfa AF: 0.0935 Hom.: 762

Bravo AF: 0.151

Asia WGS AF: 0.120 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.71
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2567768; hg19: chr8-98303151;