rs659628

Positions:

• chr13-76889101-G-A

Variant summary

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

The ENST00000613696.1(ENSG00000278727):​n.1551G>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 0.0879 in 152,272 control chromosomes in the GnomAD database, including 756 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 0.088 (756 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000613696.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.635

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 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
	ENST00000613696.1	n.1551G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0877 AC: 13337 AN: 152154 Hom.: 747 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0825

Gnomad ASJ AF: 0.0910

Gnomad EAS AF: 0.0906

Gnomad SAS AF: 0.0701

Gnomad FIN AF: 0.0412

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0576

Gnomad OTH AF: 0.0875

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0879 AC: 13380 AN: 152272 Hom.: 756 Cov.: 33 AF XY: 0.0879 AC XY: 6548 AN XY: 74460

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0825

Gnomad4 ASJ AF: 0.0910

Gnomad4 EAS AF: 0.0909

Gnomad4 SAS AF: 0.0698

Gnomad4 FIN AF: 0.0412

Gnomad4 NFE AF: 0.0576

Gnomad4 OTH AF: 0.0885

Alfa AF: 0.0659 Hom.: 367

Bravo AF: 0.0910

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs659628; hg19: chr13-77463236;