8-114997951-C-T

Variant names:

• chr8-114997951-C-T
• rs6469563
• ENST00000791004.1:n.1736C>T

Variant summary

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

The ENST00000791004.1(ENSG00000303006):​n.1736C>T 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 0.51 in 151,918 control chromosomes in the GnomAD database, including 22,351 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 (22351 hom., cov: 32)
• Consequence: ENSG00000303006 ENST00000791004.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 2 publications found

Genes affected

ENSG00000303006 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791004.1. 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
	ENSG00000303006	ENST00000791004.1		n.1736C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77409 AN: 151800 Hom.: 22290 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.510 AC: 77533 AN: 151918 Hom.: 22351 Cov.: 32 AF XY: 0.516 AC XY: 38280 AN XY: 74244

African (AFR) AF: 0.767 AC: 31790 AN: 41436

American (AMR) AF: 0.542 AC: 8270 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1216 AN: 3462

East Asian (EAS) AF: 0.777 AC: 4021 AN: 5172

South Asian (SAS) AF: 0.464 AC: 2236 AN: 4818

European-Finnish (FIN) AF: 0.404 AC: 4259 AN: 10530

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.358 AC: 24347 AN: 67930

Other (OTH) AF: 0.457 AC: 964 AN: 2108

Alfa AF: 0.398 Hom.: 21732

Bravo AF: 0.531

Asia WGS AF: 0.626 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.65
PhyloP100		-1.1

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: rs6469563;

hg19: chr8-116010180;