2-200157231-T-C

Variant names:

• chr2-200157231-T-C
• rs1569175
• ENST00000723097.1:n.186-24335A>G

Variant summary

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

The ENST00000723097.1(ENSG00000294361):​n.186-24335A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.883 in 152,190 control chromosomes in the GnomAD database, including 59,802 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 0.88 (59802 hom., cov: 31)
• Consequence: ENSG00000294361 ENST00000723097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 23 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294361	ENST00000723097.1		n.186-24335A>G		intron	N/A
	ENSG00000294361	ENST00000723098.1		n.245+17339A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.883 AC: 134283 AN: 152072 Hom.: 59762 Cov.: 31

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.926

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.942

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.883 AC: 134373 AN: 152190 Hom.: 59802 Cov.: 31 AF XY: 0.879 AC XY: 65420 AN XY: 74420

African (AFR) AF: 0.809 AC: 33594 AN: 41506

American (AMR) AF: 0.756 AC: 11568 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.926 AC: 3212 AN: 3470

East Asian (EAS) AF: 0.846 AC: 4381 AN: 5180

South Asian (SAS) AF: 0.942 AC: 4532 AN: 4810

European-Finnish (FIN) AF: 0.906 AC: 9592 AN: 10592

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64442 AN: 68024

Other (OTH) AF: 0.898 AC: 1894 AN: 2110

Alfa AF: 0.924 Hom.: 280528

Bravo AF: 0.864

Asia WGS AF: 0.886 AC: 3076 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.80
DANN	Benign	0.47
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs1569175; hg19: chr2-201021954;