rs1531577

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

ENSG00000284957 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.667 AC: 4 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 4 AN: 4

East Asian (EAS) AF: 0.750 AC: 6 AN: 8

South Asian (SAS) AF: 1.00 AC: 6 AN: 6

European-Finnish (FIN) AF: 0.438 AC: 7 AN: 16

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.753 AC: 146 AN: 194

Other (OTH) AF: 0.682 AC: 15 AN: 22

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

African (AFR) AF: 0.805 AC: 33284 AN: 41352

American (AMR) AF: 0.772 AC: 11778 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2532 AN: 3462

East Asian (EAS) AF: 0.744 AC: 3813 AN: 5124

South Asian (SAS) AF: 0.717 AC: 3454 AN: 4818

European-Finnish (FIN) AF: 0.548 AC: 5756 AN: 10510

Middle Eastern (MID) AF: 0.757 AC: 221 AN: 292

European-Non Finnish (NFE) AF: 0.673 AC: 45641 AN: 67780

Other (OTH) AF: 0.727 AC: 1530 AN: 2104

Alfa AF: 0.697 Hom.: 57143

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
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs1531577; hg19: chr8-11338561;