rs4882411

Variant names:

• chr12-84223906-A-C
• rs4882411
• ENST00000642846.1:n.35-41458A>C

Your query was ambiguous. Multiple possible variants found:

• chr12-84223906-A-C
• chr12-84223906-A-T

Variant summary

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

The ENST00000642846.1(ENSG00000257729):​n.35-41458A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 151,766 control chromosomes in the GnomAD database, including 6,670 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 0.29 (6670 hom., cov: 32)
• Consequence: ENSG00000257729 ENST00000642846.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 4 publications found

Genes affected

ENSG00000257729 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642846.1. 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
	ENSG00000257729	ENST00000642846.1		n.35-41458A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44094 AN: 151648 Hom.: 6661 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.291 AC: 44131 AN: 151766 Hom.: 6670 Cov.: 32 AF XY: 0.288 AC XY: 21337 AN XY: 74194

African (AFR) AF: 0.353 AC: 14628 AN: 41428

American (AMR) AF: 0.311 AC: 4727 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1267 AN: 3468

East Asian (EAS) AF: 0.103 AC: 533 AN: 5186

South Asian (SAS) AF: 0.227 AC: 1097 AN: 4826

European-Finnish (FIN) AF: 0.216 AC: 2272 AN: 10540

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18441 AN: 67794

Other (OTH) AF: 0.306 AC: 645 AN: 2106

Alfa AF: 0.169 Hom.: 349

Bravo AF: 0.302

Asia WGS AF: 0.178 AC: 618 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.86
DANN	Benign	0.74
PhyloP100		-0.063

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: rs4882411;

hg19: chr12-84617685;