rs4262808

chr12-107109347-G-Achr12-107109347-G-Cchr12-107109347-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, non coding transcript 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: ENST00000547679.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000547679.1	n.127+11877G>A		intron_variant, non_coding_transcript_variant		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;