rs2551649

Variant names:

• chr2-207491485-C-T
• rs2551649
• ENST00000412387.5:n.260+26135G>A

Variant summary

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

The ENST00000412387.5(ENSG00000223725):​n.260+26135G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 146,768 control chromosomes in the GnomAD database, including 14,494 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 0.39 (14494 hom., cov: 29)
• Consequence: ENSG00000223725 ENST00000412387.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

Genes affected

ENSG00000223725 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 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
ENSG00000223725	ENST00000412387.5	n.260+26135G>A		intron_variant	Intron 3 of 4	4
ENSG00000223725	ENST00000418850.1	n.256+26135G>A		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.387 AC: 56802 AN: 146650 Hom.: 14470 Cov.: 29

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.388 AC: 56878 AN: 146768 Hom.: 14494 Cov.: 29 AF XY: 0.391 AC XY: 27938 AN XY: 71516

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.363

Alfa AF: 0.332 Hom.: 5958

Asia WGS AF: 0.374 AC: 1298 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	15
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2551649; hg19: chr2-208356209;