chr2-188729897-C-T

Variant names:

• chr2-188729897-C-T
• rs10931378
• ENST00000431708.1:n.218+16527G>A

Variant summary

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

The ENST00000431708.1(ENSG00000223523):​n.218+16527G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 151,966 control chromosomes in the GnomAD database, including 35,454 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 0.68 (35454 hom., cov: 32)
• Consequence: ENSG00000223523 ENST00000431708.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 3 publications found

Genes affected

ENSG00000223523 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431708.1. 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
	ENSG00000223523	ENST00000431708.1	TSL:3	n.218+16527G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102586 AN: 151848 Hom.: 35440 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.675 AC: 102645 AN: 151966 Hom.: 35454 Cov.: 32 AF XY: 0.683 AC XY: 50728 AN XY: 74264

African (AFR) AF: 0.552 AC: 22883 AN: 41418

American (AMR) AF: 0.778 AC: 11870 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2096 AN: 3472

East Asian (EAS) AF: 0.929 AC: 4807 AN: 5172

South Asian (SAS) AF: 0.758 AC: 3656 AN: 4822

European-Finnish (FIN) AF: 0.766 AC: 8084 AN: 10556

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.688 AC: 46738 AN: 67952

Other (OTH) AF: 0.698 AC: 1471 AN: 2108

Alfa AF: 0.642 Hom.: 3663

Bravo AF: 0.674

Asia WGS AF: 0.820 AC: 2849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.12
PhyloP100		0.044

Splicing

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

Other links and lift over

dbSNP: rs10931378; hg19: chr2-189594624;