rs12486865

Positions:

• chr3-100237712-G-C

Variant summary

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

The ENST00000654821.1(ENSG00000287378):​n.195+22358C>G 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 0.274 in 151,536 control chromosomes in the GnomAD database, including 5,988 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 0.27 (5988 hom., cov: 30)
• Consequence: ENST00000654821.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

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 (NFE) allele frequency at 95% confidence interval = 0.309 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
	ENST00000654821.1	n.195+22358C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41566 AN: 151420 Hom.: 5987 Cov.: 30

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.0831

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.274 AC: 41580 AN: 151536 Hom.: 5988 Cov.: 30 AF XY: 0.270 AC XY: 19958 AN XY: 74018

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.0827

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.288

Alfa AF: 0.283 Hom.: 783

Bravo AF: 0.274

Asia WGS AF: 0.180 AC: 625 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	3.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12486865; hg19: chr3-99956556;