rs659628

Variant names:

• chr13-76889101-G-A
• rs659628
• ENST00000613696.1:n.1551G>A

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000278727 ENST00000613696.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.635
• Publications: 5 publications found

Genes affected

ENSG00000278727 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000278727	ENST00000613696.1	n.1551G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.154 AC: 6399 AN: 41524

American (AMR) AF: 0.0825 AC: 1263 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0910 AC: 316 AN: 3472

East Asian (EAS) AF: 0.0909 AC: 471 AN: 5184

South Asian (SAS) AF: 0.0698 AC: 337 AN: 4830

European-Finnish (FIN) AF: 0.0412 AC: 437 AN: 10616

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0576 AC: 3920 AN: 68026

Other (OTH) AF: 0.0885 AC: 187 AN: 2114

Alfa AF: 0.0694 Hom.: 551

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
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs659628; hg19: chr13-77463236;