rs2163314

chr12-78438806-G-Achr12-78438806-G-Cchr12-78438806-G-T

Variant summary

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

The ENST00000547569.1(ENSG00000257879):n.948+1847C>T 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 0.737 in 151,898 control chromosomes in the GnomAD database, including 41,579 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 0.74 (41579 hom., cov: 30)
• Consequence: ENST00000547569.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 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
	ENST00000547569.1	n.948+1847C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000552230.5	n.163-38587G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.737 AC: 111820 AN: 151780 Hom.: 41533 Cov.: 30

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.737 AC: 111921 AN: 151898 Hom.: 41579 Cov.: 30 AF XY: 0.740 AC XY: 54920 AN XY: 74208

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.869

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.712

Alfa AF: 0.695 Hom.: 51290

Bravo AF: 0.742

Asia WGS AF: 0.877 AC: 3051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2163314; hg19: chr12-78832586;