chr4-147126398-C-T

Variant names:

• chr4-147126398-C-T
• rs1395821
• ENST00000667105.1:n.516-22906C>T

Variant summary

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

The ENST00000667105.1(ENSG00000286371):​n.516-22906C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 151,850 control chromosomes in the GnomAD database, including 38,679 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 0.70 (38679 hom., cov: 32)
• Consequence: ENSG00000286371 ENST00000667105.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660

Genes affected

ENSG00000286371 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.804 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
ENSG00000286371	ENST00000667105.1	n.516-22906C>T		intron_variant	Intron 3 of 3
ENSG00000286371	ENST00000671296.1	n.413-31230C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106102 AN: 151732 Hom.: 38672 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.699 AC: 106131 AN: 151850 Hom.: 38679 Cov.: 32 AF XY: 0.696 AC XY: 51653 AN XY: 74224

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.717

Alfa AF: 0.787 Hom.: 70880

Bravo AF: 0.694

Asia WGS AF: 0.616 AC: 2144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1395821; hg19: chr4-148047550;