8-23668950-T-C

Variant names:

• chr8-23668950-T-C
• rs1512268
• ENST00000835202.1:n.704T>C

Variant summary

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

The ENST00000835202.1(ENSG00000308589):​n.704T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,084 control chromosomes in the GnomAD database, including 20,373 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 0.51 (20373 hom., cov: 33)
• Consequence: ENSG00000308589 ENST00000835202.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 136 publications found

Genes affected

ENSG00000308589 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835202.1. 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
	ENSG00000308589	ENST00000835202.1		n.704T>C		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000308589	ENST00000835200.1		n.475+200T>C		intron	N/A
	ENSG00000308589	ENST00000835201.1		n.1097+200T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76967 AN: 151966 Hom.: 20368 Cov.: 33

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.506 AC: 77003 AN: 152084 Hom.: 20373 Cov.: 33 AF XY: 0.506 AC XY: 37569 AN XY: 74318

African (AFR) AF: 0.358 AC: 14870 AN: 41498

American (AMR) AF: 0.536 AC: 8192 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2005 AN: 3468

East Asian (EAS) AF: 0.706 AC: 3649 AN: 5170

South Asian (SAS) AF: 0.561 AC: 2705 AN: 4818

European-Finnish (FIN) AF: 0.493 AC: 5205 AN: 10566

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38663 AN: 67960

Other (OTH) AF: 0.509 AC: 1076 AN: 2112

Alfa AF: 0.551 Hom.: 108088

Bravo AF: 0.505

Asia WGS AF: 0.563 AC: 1959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.6
DANN	Benign	0.74
PhyloP100		0.12

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: rs1512268;

hg19: chr8-23526463;