chr2-212729246-G-T

Position:

• chr2-212729246-G-T

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

(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/exons	MANE	Protein	UniProt
		n.212729246G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000273118	ENST00000415387.1	n.382-147838C>A		intron_variant		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;