ENST00000667497.1:n.163+109903A>C

Variant names:

• chr4-125862569-A-C
• rs2102317
• ENST00000667497.1:n.163+109903A>C

Variant summary

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

The ENST00000667497.1(ENSG00000250149):​n.163+109903A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 151,982 control chromosomes in the GnomAD database, including 49,934 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 0.81 (49934 hom., cov: 31)
• Consequence: ENSG00000250149 ENST00000667497.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847

Genes affected

ENSG00000250149 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 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
ENSG00000250149	ENST00000667497.1	n.163+109903A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122337 AN: 151866 Hom.: 49906 Cov.: 31

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.805 AC: 122416 AN: 151982 Hom.: 49934 Cov.: 31 AF XY: 0.801 AC XY: 59520 AN XY: 74278

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.831

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.800

Alfa AF: 0.848 Hom.: 25034

Bravo AF: 0.793

Asia WGS AF: 0.580 AC: 2019 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2102317; hg19: chr4-126783724;