2-180689841-C-T

Variant names:

• chr2-180689841-C-T
• rs1002207
• ENST00000429816.1:n.225+2389G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000429816.1(ENSG00000225258):​n.225+2389G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,008 control chromosomes in the GnomAD database, including 14,016 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 0.43 (14016 hom., cov: 32)
• Consequence: ENSG00000225258 ENST00000429816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

Genes affected

ENSG00000225258 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225258	ENST00000429816.1	n.225+2389G>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64803 AN: 151890 Hom.: 13990 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.427 AC: 64874 AN: 152008 Hom.: 14016 Cov.: 32 AF XY: 0.424 AC XY: 31475 AN XY: 74294

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.427

Alfa AF: 0.333 Hom.: 1152

Bravo AF: 0.430

Asia WGS AF: 0.438 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.7
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1002207; hg19: chr2-181554568;