13-28496864-T-C

Variant names:

• chr13-28496864-T-C
• rs664393
• ENST00000835346.1:n.1548T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000835346.1(ENSG00000279393):​n.1548T>C 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 0.889 in 152,270 control chromosomes in the GnomAD database, including 60,402 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 0.89 (60370 hom., cov: 32)
  • Exomes 𝑓: 0.91 (32 hom.)
• Consequence: ENSG00000279393 ENST00000835346.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429
• Publications: 19 publications found

Genes affected

ENSG00000279393 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835346.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000279393	ENST00000835346.1		n.1548T>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135147 AN: 152074 Hom.: 60320 Cov.: 32

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.897

GnomAD4 exome AF: 0.910 AC: 71 AN: 78 Hom.: 32 Cov.: 0 AF XY: 0.917 AC XY: 55 AN XY: 60

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.922 AC: 59 AN: 64

Other (OTH) AF: 0.667 AC: 4 AN: 6

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000406424), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.889 AC: 135257 AN: 152192 Hom.: 60370 Cov.: 32 AF XY: 0.881 AC XY: 65509 AN XY: 74382

African (AFR) AF: 0.938 AC: 38968 AN: 41548

American (AMR) AF: 0.905 AC: 13844 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.942 AC: 3269 AN: 3470

East Asian (EAS) AF: 0.707 AC: 3641 AN: 5148

South Asian (SAS) AF: 0.832 AC: 4013 AN: 4826

European-Finnish (FIN) AF: 0.763 AC: 8052 AN: 10558

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.889 AC: 60491 AN: 68018

Other (OTH) AF: 0.895 AC: 1892 AN: 2114

Alfa AF: 0.891 Hom.: 179109

Bravo AF: 0.904

Asia WGS AF: 0.811 AC: 2821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.59
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs664393; hg19: chr13-29071001;