ENST00000723097.1:n.185+31227G>A

Variant names:

• chr2-200168318-C-T
• rs4261699
• ENST00000723097.1:n.185+31227G>A

Variant summary

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

The ENST00000723097.1(ENSG00000294361):​n.185+31227G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 152,216 control chromosomes in the GnomAD database, including 61,581 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 0.90 (61581 hom., cov: 32)
• Consequence: ENSG00000294361 ENST00000723097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.456
• Publications: 1 publications found

Genes affected

ENSG00000294361 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723097.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294361	ENST00000723097.1		n.185+31227G>A		intron	N/A
	ENSG00000294361	ENST00000723098.1		n.245+6252G>A		intron	N/A
	ENSG00000294361	ENST00000723099.1		n.211-4560G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.895 AC: 136178 AN: 152098 Hom.: 61541 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.972

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.943

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.895 AC: 136270 AN: 152216 Hom.: 61581 Cov.: 32 AF XY: 0.892 AC XY: 66386 AN XY: 74432

African (AFR) AF: 0.806 AC: 33461 AN: 41510

American (AMR) AF: 0.768 AC: 11742 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.972 AC: 3370 AN: 3468

East Asian (EAS) AF: 0.848 AC: 4388 AN: 5174

South Asian (SAS) AF: 0.939 AC: 4527 AN: 4822

European-Finnish (FIN) AF: 0.943 AC: 10008 AN: 10614

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.966 AC: 65693 AN: 68026

Other (OTH) AF: 0.904 AC: 1912 AN: 2114

Alfa AF: 0.929 Hom.: 3717

Bravo AF: 0.873

Asia WGS AF: 0.892 AC: 3101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	7.1
DANN	Benign	0.55
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs4261699; hg19: chr2-201033041;