2-212746497-G-T

Variant names:

• chr2-212746497-G-T
• rs16849209
• ENST00000415387.1:n.381+146188C>A

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 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: ENSG00000273118 ENST00000415387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

Genes affected

ENSG00000273118 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000273118	ENST00000415387.1	n.381+146188C>A		intron_variant	Intron 4 of 4	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;