rs2887180

chr2-180584578-C-A

Variant summary

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

The ENST00000429816.1(ENSG00000225258):n.443-12747G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,186 control chromosomes in the GnomAD database, including 4,376 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 0.23 (4376 hom., cov: 33)
• Consequence: ENST00000429816.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000429816.1	n.443-12747G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34510 AN: 152070 Hom.: 4360 Cov.: 33

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.227 AC: 34561 AN: 152186 Hom.: 4376 Cov.: 33 AF XY: 0.233 AC XY: 17347 AN XY: 74414

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.211

Alfa AF: 0.211 Hom.: 1673

Bravo AF: 0.235

Asia WGS AF: 0.393 AC: 1366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.2
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2887180; hg19: chr2-181449305;