rs4262808

Variant names:

• chr12-107109347-G-A
• rs4262808
• ENST00000547679.1:n.127+11877G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-107109347-G-A
• chr12-107109347-G-C
• chr12-107109347-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000547679.1(ENSG00000257548):​n.127+11877G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,676 control chromosomes in the GnomAD database, including 20,362 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 0.51 (20362 hom., cov: 30)
• Consequence: ENSG00000257548 ENST00000547679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434

Genes affected

ENSG00000257548 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 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
ENSG00000257548	ENST00000547679.1	n.127+11877G>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76876 AN: 151558 Hom.: 20339 Cov.: 30

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.507 AC: 76945 AN: 151676 Hom.: 20362 Cov.: 30 AF XY: 0.511 AC XY: 37867 AN XY: 74064

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.522

Alfa AF: 0.548 Hom.: 10412

Bravo AF: 0.508

Asia WGS AF: 0.605 AC: 2103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4262808; hg19: chr12-107503125;