ENST00000415387.1:n.381+18437C>T

Variant names:

• chr2-212874248-G-A
• rs7600221
• ENST00000415387.1:n.381+18437C>T

Variant summary

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

The ENST00000415387.1(ENSG00000273118):​n.381+18437C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,082 control chromosomes in the GnomAD database, including 10,052 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 0.35 (10052 hom., cov: 32)
• Consequence: ENSG00000273118 ENST00000415387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

Genes affected

ENSG00000273118 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 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
ENSG00000273118	ENST00000415387.1	n.381+18437C>T		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53297 AN: 151964 Hom.: 10037 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.351 AC: 53328 AN: 152082 Hom.: 10052 Cov.: 32 AF XY: 0.349 AC XY: 25956 AN XY: 74358

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.362

Alfa AF: 0.378 Hom.: 15562

Bravo AF: 0.365

Asia WGS AF: 0.439 AC: 1523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7600221; hg19: chr2-213738972;