XR_007088436.1:n.373C>T

Variant names:

• chr2-241859444-C-T
• rs36084323
• XR_007088436.1:n.373C>T

Variant summary

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

The XR_007088436.1(LOC124908032):​n.373C>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 0.0599 in 152,288 control chromosomes in the GnomAD database, including 1,049 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 0.060 (1049 hom., cov: 33)
• Consequence: LOC124908032 XR_007088436.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 79 publications found

Genes affected

LOC124908032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9075 AN: 152170 Hom.: 1043 Cov.: 33

Gnomad AFR AF: 0.0464

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0118

Gnomad OTH AF: 0.0678

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

GnomAD4 genome AF: 0.0599 AC: 9116 AN: 152288 Hom.: 1049 Cov.: 33 AF XY: 0.0682 AC XY: 5077 AN XY: 74464

African (AFR) AF: 0.0468 AC: 1945 AN: 41556

American (AMR) AF: 0.179 AC: 2737 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0112 AC: 39 AN: 3470

East Asian (EAS) AF: 0.483 AC: 2489 AN: 5156

South Asian (SAS) AF: 0.0788 AC: 381 AN: 4834

European-Finnish (FIN) AF: 0.0535 AC: 568 AN: 10622

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0118 AC: 805 AN: 68022

Other (OTH) AF: 0.0704 AC: 149 AN: 2116

Alfa AF: 0.0345 Hom.: 42

Bravo AF: 0.0714

Asia WGS AF: 0.254 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.83
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs36084323; hg19: chr2-242801596;