rs286958

Variant names:

• chr5-153958488-T-C
• rs286958
• XR_001742937.1:n.124-4020A>G

Variant summary

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

The XR_001742937.1(LOC107986464):​n.124-4020A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,070 control chromosomes in the GnomAD database, including 30,533 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 0.63 (30533 hom., cov: 32)
• Consequence: LOC107986464 XR_001742937.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 4 publications found

Genes affected

LOC107986464 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95664 AN: 151952 Hom.: 30496 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.630 AC: 95746 AN: 152070 Hom.: 30533 Cov.: 32 AF XY: 0.634 AC XY: 47116 AN XY: 74312

African (AFR) AF: 0.674 AC: 27960 AN: 41456

American (AMR) AF: 0.657 AC: 10037 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2121 AN: 3470

East Asian (EAS) AF: 0.903 AC: 4680 AN: 5180

South Asian (SAS) AF: 0.563 AC: 2710 AN: 4816

European-Finnish (FIN) AF: 0.663 AC: 7003 AN: 10570

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39150 AN: 67976

Other (OTH) AF: 0.625 AC: 1320 AN: 2112

Alfa AF: 0.590 Hom.: 14607

Bravo AF: 0.639

Asia WGS AF: 0.705 AC: 2451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.66
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs286958; hg19: chr5-153338048; COSMIC: COSV60216845;