8-11480378-T-C

Variant names:

• chr8-11480378-T-C
• rs1564267
• ENST00000644741.1:n.248A>G

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284957	ENST00000644741.1	n.248A>G		non_coding_transcript_exon_variant	Exon 2 of 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;