rs1482426

Variant names:

• chr12-84127492-A-G
• rs1482426
• ENST00000688936.3:n.122+58974T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000688936.3(ENSG00000289309):​n.122+58974T>C variant causes a intron 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: ENSG00000289309 ENST00000688936.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 1 publications found

Genes affected

ENSG00000289309 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC107984536	XR_001749234.2	n.111+58974T>C		intron_variant	Intron 1 of 3
LOC107984536	XR_001749235.2	n.111+58974T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289309	ENST00000688936.3	n.122+58974T>C		intron_variant	Intron 1 of 2
ENSG00000289309	ENST00000689302.2	n.113+58974T>C		intron_variant	Intron 1 of 3
ENSG00000289309	ENST00000716306.1	n.111+58974T>C		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.0207 AC: 858 AN: 41542

American (AMR) AF: 0.164 AC: 2503 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0726 AC: 252 AN: 3470

East Asian (EAS) AF: 0.137 AC: 705 AN: 5162

South Asian (SAS) AF: 0.0967 AC: 467 AN: 4828

European-Finnish (FIN) AF: 0.165 AC: 1744 AN: 10554

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7529 AN: 67998

Other (OTH) AF: 0.107 AC: 226 AN: 2112

Alfa AF: 0.105 Hom.: 458

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1482426; hg19: chr12-84521271;