rs1402031

Variant names:

• chr4-25593908-T-C
• rs1402031
• ENST00000671933.1:n.343-14803T>C

Variant summary

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

The ENST00000671933.1(ENSG00000248545):​n.343-14803T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 152,120 control chromosomes in the GnomAD database, including 58,296 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 0.87 (58296 hom., cov: 31)
• Consequence: ENSG00000248545 ENST00000671933.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02

Genes affected

ENSG00000248545 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.952 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
ENSG00000248545	ENST00000671933.1	n.343-14803T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.873 AC: 132713 AN: 152002 Hom.: 58232 Cov.: 31

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.873 AC: 132836 AN: 152120 Hom.: 58296 Cov.: 31 AF XY: 0.874 AC XY: 64987 AN XY: 74344

Gnomad4 AFR AF: 0.960

Gnomad4 AMR AF: 0.846

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.869

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.870

Alfa AF: 0.854 Hom.: 10298

Bravo AF: 0.878

Asia WGS AF: 0.895 AC: 3115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.091
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1402031; hg19: chr4-25595530;