rs1482426

Positions:

• chr12-84127492-A-G

Variant summary

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

The ENST00000689302.1(ENSG00000289309):​n.111+58974T>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 0.0947 in 152,160 control chromosomes in the GnomAD database, including 894 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 0.095 (894 hom., cov: 32)
• Consequence: ENST00000689302.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984536	XR_001749235.2	n.111+58974T>C		intron_variant, non_coding_transcript_variant
LOC107984536	XR_001749234.2	n.111+58974T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000689302.1	n.111+58974T>C		intron_variant, non_coding_transcript_variant
	ENST00000688936.2	n.111+58974T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0947 AC: 14396 AN: 152042 Hom.: 893 Cov.: 32

Gnomad AFR AF: 0.0207

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0956

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0947 AC: 14411 AN: 152160 Hom.: 894 Cov.: 32 AF XY: 0.0988 AC XY: 7348 AN XY: 74380

Gnomad4 AFR AF: 0.0207

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.0726

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.0967

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.107

Alfa AF: 0.105 Hom.: 422

Bravo AF: 0.0918

Asia WGS AF: 0.0880 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1482426; hg19: chr12-84521271;