rs1531577

Variant names:

• chr8-11481052-C-T
• rs1531577
• ENST00000644741.1:n.17G>A

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284957	ENST00000644741.1	n.17G>A		non_coding_transcript_exon_variant	Exon 1 of 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;