chr13-97433095-G-A

Variant names:

• chr13-97433095-G-A
• rs1159278
• ENST00000659310.1:n.900C>T

Variant summary

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

The ENST00000659310.1(ENSG00000286416):​n.900C>T 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 0.54 in 152,008 control chromosomes in the GnomAD database, including 25,806 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 0.54 (25806 hom., cov: 33)
• Consequence: ENSG00000286416 ENST00000659310.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 6 publications found

Genes affected

ENSG00000286416 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.679 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
ENSG00000286416	ENST00000659310.1	n.900C>T		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000286416	ENST00000662529.1	n.864C>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000286416	ENST00000814909.1	n.895C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82131 AN: 151888 Hom.: 25805 Cov.: 33

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.603

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.540 AC: 82148 AN: 152008 Hom.: 25806 Cov.: 33 AF XY: 0.546 AC XY: 40566 AN XY: 74296

African (AFR) AF: 0.202 AC: 8401 AN: 41510

American (AMR) AF: 0.647 AC: 9896 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2619 AN: 3468

East Asian (EAS) AF: 0.414 AC: 2133 AN: 5156

South Asian (SAS) AF: 0.685 AC: 3297 AN: 4816

European-Finnish (FIN) AF: 0.674 AC: 7093 AN: 10530

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46447 AN: 67926

Other (OTH) AF: 0.605 AC: 1281 AN: 2116

Alfa AF: 0.653 Hom.: 28221

Bravo AF: 0.522

Asia WGS AF: 0.524 AC: 1824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.7
DANN	Benign	0.93
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1159278; hg19: chr13-98085349;