2-200168318-C-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906112	XR_007088012.1	n.228+6252G>A		intron_variant	Intron 1 of 2
LOC124906112	XR_007088015.1	n.228+6252G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294361	ENST00000723097.1	n.185+31227G>A		intron_variant	Intron 1 of 4
ENSG00000294361	ENST00000723098.1	n.245+6252G>A		intron_variant	Intron 1 of 1
ENSG00000294361	ENST00000723099.1	n.211-4560G>A		intron_variant	Intron 1 of 1

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 v4.3

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;