8-11480378-T-C

Position:

• chr8-11480378-T-C

Variant summary

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

The ENST00000644741.1(ENSG00000284957):​n.248A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,020 control chromosomes in the GnomAD database, including 42,312 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 (42299 hom., cov: 31)
  • Exomes 𝑓: 0.72 (13 hom.)
• Consequence: ENSG00000284957 ENST00000644741.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750

Genes affected

ENSG00000284957 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.11480378T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000284957	ENST00000644741.1	n.248A>G		non_coding_transcript_exon_variant	2/3

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111728 AN: 151862 Hom.: 42277 Cov.: 31

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.758

GnomAD4 exome AF: 0.725 AC: 29 AN: 40 Hom.: 13 Cov.: 0 AF XY: 0.885 AC XY: 23 AN XY: 26

Gnomad4 AFR exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.867

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.736 AC: 111794 AN: 151980 Hom.: 42299 Cov.: 31 AF XY: 0.730 AC XY: 54240 AN XY: 74272

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.830

Gnomad4 OTH AF: 0.762

Alfa AF: 0.796 Hom.: 20026

Bravo AF: 0.738

Asia WGS AF: 0.778 AC: 2705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1564267; hg19: chr8-11337887;