rs72954151

Variant names:

• chr2-207490606-A-G
• rs72954151
• ENST00000412387.5:n.260+27014T>C

Variant summary

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

The ENST00000412387.5(ENSG00000223725):​n.260+27014T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 146,340 control chromosomes in the GnomAD database, including 13,116 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 0.37 (13116 hom., cov: 28)
• Consequence: ENSG00000223725 ENST00000412387.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595

Genes affected

ENSG00000223725 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.424 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+27014T>C		intron_variant	Intron 3 of 4	4
ENSG00000223725	ENST00000418850.1	n.256+27014T>C		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.367 AC: 53600 AN: 146218 Hom.: 13098 Cov.: 28

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.319

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.367 AC: 53668 AN: 146340 Hom.: 13116 Cov.: 28 AF XY: 0.371 AC XY: 26456 AN XY: 71398

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.354

Alfa AF: 0.363 Hom.: 1486

Asia WGS AF: 0.372 AC: 1293 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72954151; hg19: chr2-208355330;