8-2176139-C-T

Variant names:

• chr8-2176139-C-T
• rs2119237
• ENST00000685917.3:n.113-6860C>T

Variant summary

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

The ENST00000685917.3(ENSG00000288782):​n.113-6860C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,128 control chromosomes in the GnomAD database, including 1,854 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 (1854 hom., cov: 33)
• Consequence: ENSG00000288782 ENST00000685917.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.544
• Publications: 0 publications found

Genes affected

ENSG00000288782 (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 (SAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685917.3. 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
	ENSG00000288782	ENST00000685917.3		n.113-6860C>T		intron	N/A
	ENSG00000288782	ENST00000776942.1		n.130-16796C>T		intron	N/A
	ENSG00000288782	ENST00000776943.1		n.128-8812C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20695 AN: 152010 Hom.: 1851 Cov.: 33

Gnomad AFR AF: 0.0312

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.136 AC: 20707 AN: 152128 Hom.: 1854 Cov.: 33 AF XY: 0.143 AC XY: 10601 AN XY: 74378

African (AFR) AF: 0.0311 AC: 1294 AN: 41548

American (AMR) AF: 0.120 AC: 1828 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1249 AN: 5166

South Asian (SAS) AF: 0.310 AC: 1496 AN: 4822

European-Finnish (FIN) AF: 0.235 AC: 2477 AN: 10552

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11316 AN: 67966

Other (OTH) AF: 0.132 AC: 279 AN: 2114

Alfa AF: 0.0801 Hom.: 307

Bravo AF: 0.119

Asia WGS AF: 0.214 AC: 744 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	1.8
DANN	Benign	0.82
PhyloP100		0.54

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: rs2119237;

hg19: chr8-2124329;