5-81876393-T-C

Variant names:

• chr5-81876393-T-C
• rs6452434
• XR_007058843.1:n.329+873T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007058843.1(LOC124901018):​n.329+873T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.93 in 151,998 control chromosomes in the GnomAD database, including 66,157 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 0.93 (66157 hom., cov: 30)
• Consequence: LOC124901018 XR_007058843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

LOC124901018 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901018	XR_007058843.1	n.329+873T>C		intron_variant	Intron 3 of 5
LOC124901018	XR_007058844.1	n.231-16293T>C		intron_variant	Intron 2 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.930 AC: 141288 AN: 151878 Hom.: 66114 Cov.: 30

Gnomad AFR AF: 0.967

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.930 AC: 141377 AN: 151998 Hom.: 66157 Cov.: 30 AF XY: 0.927 AC XY: 68864 AN XY: 74294

Gnomad4 AFR AF: 0.967

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.916

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.906

Gnomad4 FIN AF: 0.952

Gnomad4 NFE AF: 0.953

Gnomad4 OTH AF: 0.911

Alfa AF: 0.938 Hom.: 89137

Bravo AF: 0.916

Asia WGS AF: 0.819 AC: 2842 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6452434; hg19: chr5-81172212;