rs1531577

Positions:

• chr8-11481052-C-T

Variant summary

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

The ENST00000644741.1(ENSG00000284957):​n.17G>A 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 0.716 in 151,854 control chromosomes in the GnomAD database, including 39,340 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 0.72 (39266 hom., cov: 31)
  • Exomes 𝑓: 0.74 (74 hom.)
• Consequence: ENSG00000284957 ENST00000644741.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.53

Genes affected

ENSG00000284957 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.11481052C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000284957	ENST00000644741.1	n.17G>A		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108438 AN: 151478 Hom.: 39215 Cov.: 31

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.723

GnomAD4 exome AF: 0.736 AC: 190 AN: 258 Hom.: 74 Cov.: 0 AF XY: 0.745 AC XY: 149 AN XY: 200

Gnomad4 AFR exome AF: 0.667

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.438

Gnomad4 NFE exome AF: 0.753

Gnomad4 OTH exome AF: 0.682

GnomAD4 genome AF: 0.716 AC: 108551 AN: 151596 Hom.: 39266 Cov.: 31 AF XY: 0.712 AC XY: 52758 AN XY: 74098

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.727

Alfa AF: 0.703 Hom.: 8393

Bravo AF: 0.738

Asia WGS AF: 0.768 AC: 2672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.042
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1531577; hg19: chr8-11338561;