13-21661445-A-G

Variant names:

• chr13-21661445-A-G
• rs829209
• ENST00000701135.2:n.277+9152T>C

Variant summary

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

The ENST00000701135.2(ENSG00000289860):​n.277+9152T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 151,948 control chromosomes in the GnomAD database, including 26,882 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 0.59 (26882 hom., cov: 31)
• Consequence: ENSG00000289860 ENST00000701135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 5 publications found

Genes affected

ENSG00000289860 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 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
ENSG00000289860	ENST00000701135.2	n.277+9152T>C		intron_variant	Intron 2 of 2
ENSG00000289860	ENST00000753720.1	n.310+9152T>C		intron_variant	Intron 1 of 1
ENSG00000289860	ENST00000753721.1	n.352+9152T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89604 AN: 151830 Hom.: 26839 Cov.: 31

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.590 AC: 89695 AN: 151948 Hom.: 26882 Cov.: 31 AF XY: 0.581 AC XY: 43185 AN XY: 74278

African (AFR) AF: 0.670 AC: 27754 AN: 41424

American (AMR) AF: 0.429 AC: 6556 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1529 AN: 3468

East Asian (EAS) AF: 0.510 AC: 2627 AN: 5152

South Asian (SAS) AF: 0.549 AC: 2641 AN: 4814

European-Finnish (FIN) AF: 0.574 AC: 6058 AN: 10548

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40752 AN: 67954

Other (OTH) AF: 0.559 AC: 1180 AN: 2110

Alfa AF: 0.566 Hom.: 12561

Bravo AF: 0.586

Asia WGS AF: 0.555 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.64
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs829209; hg19: chr13-22235584;