2-212746497-G-T

Position:

• chr2-212746497-G-T

Variant summary

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

The ENST00000415387.1(ENSG00000273118):​n.381+146188C>A 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 0.229 in 151,900 control chromosomes in the GnomAD database, including 4,120 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 0.23 (4120 hom., cov: 32)
• Consequence: ENST00000415387.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000415387.1	n.381+146188C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34665 AN: 151782 Hom.: 4109 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.229 AC: 34716 AN: 151900 Hom.: 4120 Cov.: 32 AF XY: 0.225 AC XY: 16720 AN XY: 74244

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.209

Alfa AF: 0.224 Hom.: 3859

Bravo AF: 0.236

Asia WGS AF: 0.202 AC: 701 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.56
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16849209; hg19: chr2-213611221;