rs7589138

Variant names:

• chr2-120338344-T-C
• rs7589138
• XM_047446882.1:c.142-5578T>C

Variant summary

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

The XM_047446882.1(LOC105373989):​c.142-5578T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,184 control chromosomes in the GnomAD database, including 22,067 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 0.51 (22067 hom., cov: 34)
• Consequence: LOC105373989 XM_047446882.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190
• Publications: 6 publications found

Genes affected

LOC105373989 (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 (AFR) allele frequency at 95% confidence interval = 0.75 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: 0.514 AC: 78224 AN: 152066 Hom.: 22017 Cov.: 34

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.515 AC: 78338 AN: 152184 Hom.: 22067 Cov.: 34 AF XY: 0.510 AC XY: 37963 AN XY: 74400

African (AFR) AF: 0.757 AC: 31418 AN: 41524

American (AMR) AF: 0.495 AC: 7572 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1620 AN: 3472

East Asian (EAS) AF: 0.289 AC: 1501 AN: 5188

South Asian (SAS) AF: 0.544 AC: 2622 AN: 4820

European-Finnish (FIN) AF: 0.344 AC: 3642 AN: 10596

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28279 AN: 67976

Other (OTH) AF: 0.504 AC: 1065 AN: 2114

Alfa AF: 0.444 Hom.: 44609

Bravo AF: 0.530

Asia WGS AF: 0.498 AC: 1731 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	0.45
DANN	Benign	0.74
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs7589138; hg19: chr2-121095920;