5-153958488-T-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986464	XR_001742937.1	n.124-4020A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;