rs12619285

Positions:

• chr2-212959321-A-G

Variant summary

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

The ENST00000415387.1(ENSG00000273118):​n.82-55878T>C 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 0.317 in 152,000 control chromosomes in the GnomAD database, including 8,384 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 0.32 (8384 hom., cov: 32)
• Consequence: ENST00000415387.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130

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 (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102725082	XR_007088066.1	n.17410+6063T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000415387.1	n.82-55878T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48078 AN: 151882 Hom.: 8376 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.317 AC: 48117 AN: 152000 Hom.: 8384 Cov.: 32 AF XY: 0.322 AC XY: 23907 AN XY: 74290

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.316

Alfa AF: 0.282 Hom.: 14513

Bravo AF: 0.338

Asia WGS AF: 0.399 AC: 1391 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	8.7
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12619285; hg19: chr2-213824045;