rs2394186

Variant names:

• chr6-29848644-A-G
• rs2394186
• XR_926680.3:n.2192T>C

Variant summary

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

The XR_926680.3(LOC105375010):​n.2192T>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 0.161 in 152,210 control chromosomes in the GnomAD database, including 2,007 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 0.16 (2007 hom., cov: 33)
• Consequence: LOC105375010 XR_926680.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 22 publications found

Genes affected

LOC105375010 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24545 AN: 152092 Hom.: 2002 Cov.: 33

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.161 AC: 24554 AN: 152210 Hom.: 2007 Cov.: 33 AF XY: 0.160 AC XY: 11913 AN XY: 74410

African (AFR) AF: 0.145 AC: 6029 AN: 41536

American (AMR) AF: 0.185 AC: 2829 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3466

East Asian (EAS) AF: 0.212 AC: 1100 AN: 5180

South Asian (SAS) AF: 0.156 AC: 753 AN: 4820

European-Finnish (FIN) AF: 0.135 AC: 1434 AN: 10594

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11266 AN: 68018

Other (OTH) AF: 0.159 AC: 336 AN: 2110

Alfa AF: 0.166 Hom.: 8748

Bravo AF: 0.164

Asia WGS AF: 0.261 AC: 905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.45
PhyloP100		-1.9

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: rs2394186;

hg19: chr6-29816421;