13-106286062-A-T

Variant names:

• chr13-106286062-A-T
• rs354439
• ENST00000669705.1:n.70-26411T>A

Variant summary

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

The ENST00000669705.1(ENSG00000286780):​n.70-26411T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 152,000 control chromosomes in the GnomAD database, including 17,282 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 0.46 (17282 hom., cov: 32)
• Consequence: ENSG00000286780 ENST00000669705.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.60

Genes affected

ENSG00000286780 (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 = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984626	XR_001750000.2	n.187-1256T>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286780	ENST00000669705.1	n.70-26411T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70368 AN: 151882 Hom.: 17237 Cov.: 32

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.464 AC: 70462 AN: 152000 Hom.: 17282 Cov.: 32 AF XY: 0.460 AC XY: 34183 AN XY: 74284

African (AFR) AF: 0.621 AC: 25720 AN: 41434

American (AMR) AF: 0.363 AC: 5542 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1952 AN: 3470

East Asian (EAS) AF: 0.438 AC: 2262 AN: 5164

South Asian (SAS) AF: 0.618 AC: 2974 AN: 4812

European-Finnish (FIN) AF: 0.337 AC: 3558 AN: 10564

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26899 AN: 67972

Other (OTH) AF: 0.457 AC: 964 AN: 2110

Alfa AF: 0.435 Hom.: 1871

Bravo AF: 0.470

Asia WGS AF: 0.523 AC: 1817 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0030
DANN	Benign	0.57
PhyloP100		-3.6

Splicing

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

Publications

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Other links and lift over

dbSNP: rs354439; hg19: chr13-106938411;