XR_007087259.1:n.4906C>T

Variant names:

• chr2-148526499-C-T
• rs1108567
• XR_007087259.1:n.4906C>T

Variant summary

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

The XR_007087259.1(LOC124907896):​n.4906C>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 0.751 in 151,716 control chromosomes in the GnomAD database, including 43,814 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 0.75 (43814 hom., cov: 29)
• Consequence: LOC124907896 XR_007087259.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• Publications: 11 publications found

Genes affected

LOC124907896 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.786 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: 0.751 AC: 113854 AN: 151598 Hom.: 43799 Cov.: 29

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.751 AC: 113910 AN: 151716 Hom.: 43814 Cov.: 29 AF XY: 0.744 AC XY: 55115 AN XY: 74122

African (AFR) AF: 0.789 AC: 32620 AN: 41348

American (AMR) AF: 0.653 AC: 9955 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2483 AN: 3470

East Asian (EAS) AF: 0.291 AC: 1488 AN: 5112

South Asian (SAS) AF: 0.564 AC: 2694 AN: 4778

European-Finnish (FIN) AF: 0.780 AC: 8215 AN: 10532

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53773 AN: 67914

Other (OTH) AF: 0.757 AC: 1595 AN: 2108

Alfa AF: 0.773 Hom.: 59482

Bravo AF: 0.740

Asia WGS AF: 0.444 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.73
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs1108567; hg19: chr2-149284068;