12-76695101-A-G

Variant names:

• chr12-76695101-A-G
• rs6539583
• ENST00000832799.1:n.703+3996A>G

Variant summary

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

The ENST00000832799.1(ENSG00000257526):​n.703+3996A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 151,998 control chromosomes in the GnomAD database, including 29,555 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 0.62 (29555 hom., cov: 31)
• Consequence: ENSG00000257526 ENST00000832799.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803
• Publications: 5 publications found

Genes affected

ENSG00000257526 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832799.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257526	ENST00000832799.1		n.703+3996A>G		intron	N/A
	ENSG00000257526	ENST00000832800.1		n.565-22806A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94243 AN: 151880 Hom.: 29541 Cov.: 31

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.620 AC: 94289 AN: 151998 Hom.: 29555 Cov.: 31 AF XY: 0.618 AC XY: 45875 AN XY: 74254

African (AFR) AF: 0.687 AC: 28471 AN: 41456

American (AMR) AF: 0.553 AC: 8453 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2173 AN: 3472

East Asian (EAS) AF: 0.623 AC: 3206 AN: 5150

South Asian (SAS) AF: 0.567 AC: 2730 AN: 4816

European-Finnish (FIN) AF: 0.601 AC: 6336 AN: 10542

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40960 AN: 67958

Other (OTH) AF: 0.611 AC: 1291 AN: 2114

Alfa AF: 0.606 Hom.: 118056

Bravo AF: 0.620

Asia WGS AF: 0.566 AC: 1971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.28
PhyloP100		-0.80

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6539583;

hg19: chr12-77088881;