XR_939013.3:n.678C>T

Variant names:

• chr4-98183728-G-A
• rs13134014
• XR_939013.3:n.678C>T

Variant summary

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

The XR_939013.3(LOC105377340):​n.678C>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 0.16 in 151,990 control chromosomes in the GnomAD database, including 2,092 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 (2092 hom., cov: 31)
• Consequence: LOC105377340 XR_939013.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 2 publications found

Genes affected

LOC105377340 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.27 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: 0.160 AC: 24276 AN: 151870 Hom.: 2093 Cov.: 31

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.160 AC: 24296 AN: 151990 Hom.: 2092 Cov.: 31 AF XY: 0.159 AC XY: 11796 AN XY: 74294

African (AFR) AF: 0.120 AC: 4976 AN: 41436

American (AMR) AF: 0.153 AC: 2329 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 602 AN: 3466

East Asian (EAS) AF: 0.233 AC: 1204 AN: 5168

South Asian (SAS) AF: 0.283 AC: 1362 AN: 4816

European-Finnish (FIN) AF: 0.109 AC: 1149 AN: 10570

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12004 AN: 67950

Other (OTH) AF: 0.177 AC: 375 AN: 2114

Alfa AF: 0.173 Hom.: 5344

Bravo AF: 0.159

Asia WGS AF: 0.305 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.59
PhyloP100		0.12

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13134014; hg19: chr4-99104879;