2-212729246-G-T

Variant names:

• chr2-212729246-G-T
• rs7565158
• ENST00000415387.1:n.382-147838C>A

Variant summary

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

The ENST00000415387.1(ENSG00000273118):​n.382-147838C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,716 control chromosomes in the GnomAD database, including 26,754 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 0.57 (26754 hom., cov: 30)
• Consequence: ENSG00000273118 ENST00000415387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

ENSG00000273118 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 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.382-147838C>A		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86840 AN: 151598 Hom.: 26747 Cov.: 30

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.573 AC: 86868 AN: 151716 Hom.: 26754 Cov.: 30 AF XY: 0.569 AC XY: 42173 AN XY: 74132

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.596

Alfa AF: 0.677 Hom.: 73332

Bravo AF: 0.546

Asia WGS AF: 0.495 AC: 1720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7565158; hg19: chr2-213593970;