XR_001745736.2:n.3385T>C

Variant names:

• chr8-115916875-T-C
• rs4598283
• XR_001745736.2:n.3385T>C

Variant summary

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

The XR_001745736.2(LOC107986902):​n.3385T>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 0.144 in 152,250 control chromosomes in the GnomAD database, including 2,474 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 (2474 hom., cov: 32)
• Consequence: LOC107986902 XR_001745736.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 3 publications found

Genes affected

LOC107986902 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.282 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: 0.144 AC: 21851 AN: 152132 Hom.: 2464 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.144 AC: 21887 AN: 152250 Hom.: 2474 Cov.: 32 AF XY: 0.147 AC XY: 10979 AN XY: 74436

African (AFR) AF: 0.267 AC: 11077 AN: 41496

American (AMR) AF: 0.289 AC: 4427 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0565 AC: 196 AN: 3472

East Asian (EAS) AF: 0.115 AC: 596 AN: 5176

South Asian (SAS) AF: 0.161 AC: 779 AN: 4824

European-Finnish (FIN) AF: 0.0263 AC: 280 AN: 10628

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0596 AC: 4057 AN: 68030

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

Alfa AF: 0.110 Hom.: 200

Bravo AF: 0.167

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.64
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs4598283; hg19: chr8-116929100;