rs952148

Variant names:

• chr8-20234008-G-A
• rs952148
• ENST00000846276.1:n.115+692C>T

Variant summary

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

The ENST00000846276.1(ENSG00000309971):​n.115+692C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,264 control chromosomes in the GnomAD database, including 1,055 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 0.11 (1055 hom., cov: 32)
• Consequence: ENSG00000309971 ENST00000846276.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.935
• Publications: 2 publications found

Genes affected

ENSG00000309971 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846276.1. 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
	ENSG00000309971	ENST00000846276.1		n.115+692C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16850 AN: 152146 Hom.: 1055 Cov.: 32

Gnomad AFR AF: 0.0788

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.0556

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0847

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.111 AC: 16846 AN: 152264 Hom.: 1055 Cov.: 32 AF XY: 0.111 AC XY: 8259 AN XY: 74454

African (AFR) AF: 0.0787 AC: 3269 AN: 41554

American (AMR) AF: 0.174 AC: 2668 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0556 AC: 193 AN: 3470

East Asian (EAS) AF: 0.122 AC: 630 AN: 5180

South Asian (SAS) AF: 0.149 AC: 719 AN: 4824

European-Finnish (FIN) AF: 0.0847 AC: 898 AN: 10608

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8164 AN: 68010

Other (OTH) AF: 0.108 AC: 228 AN: 2110

Alfa AF: 0.114 Hom.: 1993

Bravo AF: 0.113

Asia WGS AF: 0.137 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.92
DANN	Benign	0.75
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs952148; hg19: chr8-20091519;