chr12-84127492-A-G

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000688936.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289309	ENST00000688936.3		n.122+58974T>C		intron	N/A
	ENSG00000289309	ENST00000689302.2		n.113+58974T>C		intron	N/A
	ENSG00000289309	ENST00000716306.1		n.111+58974T>C		intron	N/A

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 v4.9

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;