chr8-15952312-T-C

Position:

• chr8-15952312-T-C

Variant summary

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

The ENST00000664439.1(ENSG00000287476):​n.163+13033A>G 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 0.873 in 152,078 control chromosomes in the GnomAD database, including 59,034 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 0.87 (59034 hom., cov: 31)
• Consequence: ENST00000664439.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.604

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000664439.1	n.163+13033A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.873 AC: 132700 AN: 151960 Hom.: 59012 Cov.: 31

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.977

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.943

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.891

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

GnomAD4 genome AF: 0.873 AC: 132769 AN: 152078 Hom.: 59034 Cov.: 31 AF XY: 0.872 AC XY: 64842 AN XY: 74328

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.943

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.955

Gnomad4 NFE AF: 0.973

Gnomad4 OTH AF: 0.891

Alfa AF: 0.951 Hom.: 85027

Bravo AF: 0.855

Asia WGS AF: 0.848 AC: 2949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.3
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7829952; hg19: chr8-15809821;