2-188729897-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373790	XR_923685.3	n.112-8695C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223523	ENST00000431708.1	n.218+16527G>A		intron_variant	Intron 2 of 7	3

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 v4.3

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;