2-212874248-G-A

Position:

• chr2-212874248-G-A

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, non coding transcript 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: ENST00000415387.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000415387.1	n.381+18437C>T		intron_variant, non_coding_transcript_variant		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;