5-81876393-T-C

Variant names:

• chr5-81876393-T-C
• rs6452434
• ENST00000781317.1:n.298-16293T>C

Variant summary

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

The ENST00000781317.1(ENSG00000287938):​n.298-16293T>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: ENSG00000287938 ENST00000781317.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 1 publications found

Genes affected

ENSG00000287938 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000287938	ENST00000781317.1	n.298-16293T>C		intron_variant	Intron 3 of 3
ENSG00000287938	ENST00000781318.1	n.272-16293T>C		intron_variant	Intron 2 of 2
ENSG00000287938	ENST00000781319.1	n.251+873T>C		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.967 AC: 40059 AN: 41434

American (AMR) AF: 0.772 AC: 11791 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3178 AN: 3470

East Asian (EAS) AF: 0.787 AC: 4060 AN: 5156

South Asian (SAS) AF: 0.906 AC: 4349 AN: 4802

European-Finnish (FIN) AF: 0.952 AC: 10030 AN: 10538

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.953 AC: 64823 AN: 68014

Other (OTH) AF: 0.911 AC: 1923 AN: 2110

Alfa AF: 0.939 Hom.: 202533

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6452434; hg19: chr5-81172212;