rs2166842

Variant names:

• chr8-567596-A-C
• rs2166842
• ENST00000729109.1:n.365+4787A>C

Variant summary

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

The ENST00000729109.1(ENSG00000295301):​n.365+4787A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,174 control chromosomes in the GnomAD database, including 3,581 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 0.20 (3581 hom., cov: 32)
• Consequence: ENSG00000295301 ENST00000729109.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 2 publications found

Genes affected

ENSG00000295301 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729109.1. 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
	ENSG00000295301	ENST00000729109.1		n.365+4787A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31123 AN: 152056 Hom.: 3559 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.205 AC: 31191 AN: 152174 Hom.: 3581 Cov.: 32 AF XY: 0.204 AC XY: 15150 AN XY: 74400

African (AFR) AF: 0.307 AC: 12737 AN: 41514

American (AMR) AF: 0.212 AC: 3235 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 407 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1703 AN: 5174

South Asian (SAS) AF: 0.137 AC: 661 AN: 4824

European-Finnish (FIN) AF: 0.136 AC: 1444 AN: 10586

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10470 AN: 67996

Other (OTH) AF: 0.192 AC: 406 AN: 2114

Alfa AF: 0.173 Hom.: 6752

Bravo AF: 0.216

Asia WGS AF: 0.209 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.15
DANN	Benign	0.68
PhyloP100		-1.4

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: rs2166842;

hg19: chr8-517596;