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. Variant got -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

Genes affected

ENSG00000257729 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257729	ENST00000642846.1	n.35-41458A>C		intron_variant	Intron 1 of 7

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

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.306

Alfa AF: 0.158 Hom.: 297

Bravo AF: 0.302

Asia WGS AF: 0.178 AC: 618 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4882411; hg19: chr12-84617685;