rs2126736

Variant names:

• chr5-75279159-A-G
• rs2126736
• XR_007058824.1:n.182-3654T>C

Variant summary

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

The XR_007058824.1(LOC124901007):​n.182-3654T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,034 control chromosomes in the GnomAD database, including 19,075 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 0.49 (19075 hom., cov: 32)
• Consequence: LOC124901007 XR_007058824.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 3 publications found

Genes affected

LOC124901007 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 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: 0.493 AC: 74956 AN: 151916 Hom.: 19044 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.494 AC: 75050 AN: 152034 Hom.: 19075 Cov.: 32 AF XY: 0.497 AC XY: 36930 AN XY: 74312

African (AFR) AF: 0.616 AC: 25525 AN: 41428

American (AMR) AF: 0.464 AC: 7096 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1792 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2885 AN: 5180

South Asian (SAS) AF: 0.599 AC: 2891 AN: 4824

European-Finnish (FIN) AF: 0.450 AC: 4748 AN: 10556

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28584 AN: 67978

Other (OTH) AF: 0.495 AC: 1046 AN: 2114

Alfa AF: 0.448 Hom.: 61289

Bravo AF: 0.497

Asia WGS AF: 0.613 AC: 2130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.60
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2126736; hg19: chr5-74574984;