rs12619696

chr2-46463303-G-Achr2-46463303-G-C

Variant summary

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

The ENST00000517716.2(ENSG00000253515):n.79+33100G>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 0.151 in 152,110 control chromosomes in the GnomAD database, including 3,348 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 0.15 (3348 hom., cov: 32)
• Consequence: ENST00000517716.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 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
	ENST00000517716.2	n.79+33100G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22962 AN: 151992 Hom.: 3343 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0317

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.151 AC: 22986 AN: 152110 Hom.: 3348 Cov.: 32 AF XY: 0.155 AC XY: 11527 AN XY: 74360

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0316

Gnomad4 OTH AF: 0.136

Alfa AF: 0.135 Hom.: 475

Bravo AF: 0.166

Asia WGS AF: 0.332 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	6.8
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12619696; hg19: chr2-46690442;