ENST00000667497.1:n.163+112661A>C

Variant names:

• chr4-125865327-A-C
• rs10031803
• ENST00000667497.1:n.163+112661A>C

Variant summary

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

The ENST00000667497.1(ENSG00000250149):​n.163+112661A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,058 control chromosomes in the GnomAD database, including 49,974 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 (49974 hom., cov: 31)
• Consequence: ENSG00000250149 ENST00000667497.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 0 publications found

Genes affected

ENSG00000250149 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667497.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250149	ENST00000667497.1		n.163+112661A>C		intron	N/A
	ENSG00000300351	ENST00000771109.1		n.212+19237A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122423 AN: 151940 Hom.: 49946 Cov.: 31

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.814

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: 0.806 AC: 122503 AN: 152058 Hom.: 49974 Cov.: 31 AF XY: 0.801 AC XY: 59558 AN XY: 74326

African (AFR) AF: 0.768 AC: 31872 AN: 41496

American (AMR) AF: 0.696 AC: 10636 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2885 AN: 3472

East Asian (EAS) AF: 0.551 AC: 2828 AN: 5132

South Asian (SAS) AF: 0.716 AC: 3454 AN: 4822

European-Finnish (FIN) AF: 0.814 AC: 8597 AN: 10556

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59445 AN: 67988

Other (OTH) AF: 0.800 AC: 1690 AN: 2112

Alfa AF: 0.847 Hom.: 22621

Bravo AF: 0.793

Asia WGS AF: 0.580 AC: 2022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.58
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs10031803; hg19: chr4-126786482;