8-11480957-C-T

Position:

• chr8-11480957-C-T

Variant summary

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

The ENST00000644741.1(ENSG00000284957):​n.64+48G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,772 control chromosomes in the GnomAD database, including 7,659 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 0.29 (7654 hom., cov: 30)
  • Exomes 𝑓: 0.14 (5 hom.)
• Consequence: ENSG00000284957 ENST00000644741.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

Genes affected

ENSG00000284957 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 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
ENSG00000284957	ENST00000644741.1	n.64+48G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44429 AN: 151488 Hom.: 7637 Cov.: 30

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.143 AC: 24 AN: 168 Hom.: 5 Cov.: 0 AF XY: 0.117 AC XY: 15 AN XY: 128

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.100

Gnomad4 NFE exome AF: 0.119

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.293 AC: 44455 AN: 151604 Hom.: 7654 Cov.: 30 AF XY: 0.300 AC XY: 22260 AN XY: 74086

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.306

Alfa AF: 0.136 Hom.: 247

Bravo AF: 0.308

Asia WGS AF: 0.581 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
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: rs35393613; hg19: chr8-11338466;