4-105084090-C-T

Variant names:

• chr4-105084090-C-T
• rs10008015
• ENST00000506148.5:n.455+22616C>T

Variant summary

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

The ENST00000506386.1(ENSG00000248373):​n.319+22616C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.924 in 152,068 control chromosomes in the GnomAD database, including 64,965 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 0.92 (64965 hom., cov: 32)
• Consequence: ENSG00000248373 ENST00000506386.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

ENSG00000248373 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248373	ENST00000506148.5	n.455+22616C>T		intron_variant	Intron 3 of 3	5
ENSG00000248373	ENST00000506386.1	n.319+22616C>T		intron_variant	Intron 2 of 3	3
ENSG00000248373	ENST00000671069.1	n.884+22616C>T		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140330 AN: 151950 Hom.: 64910 Cov.: 32

Gnomad AFR AF: 0.979

Gnomad AMI AF: 0.973

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.956

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.894

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.924 AC: 140441 AN: 152068 Hom.: 64965 Cov.: 32 AF XY: 0.926 AC XY: 68856 AN XY: 74330

Gnomad4 AFR AF: 0.979

Gnomad4 AMR AF: 0.891

Gnomad4 ASJ AF: 0.903

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.937

Gnomad4 FIN AF: 0.956

Gnomad4 NFE AF: 0.894

Gnomad4 OTH AF: 0.895

Alfa AF: 0.905 Hom.: 33296

Bravo AF: 0.921

Asia WGS AF: 0.918 AC: 3194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.050
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10008015; hg19: chr4-106005247;