chr13-80997555-G-A

Variant names:

• chr13-80997555-G-A
• rs11616409
• ENST00000655229.1:n.43-11076C>T

Variant summary

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

The ENST00000655229.1(ENSG00000286746):​n.43-11076C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,038 control chromosomes in the GnomAD database, including 7,324 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 0.29 (7324 hom., cov: 32)
• Consequence: ENSG00000286746 ENST00000655229.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 3 publications found

Genes affected

ENSG00000286746 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655229.1. 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
	ENSG00000286746	ENST00000655229.1		n.43-11076C>T		intron	N/A
	ENSG00000286746	ENST00000660876.1		n.53+20125C>T		intron	N/A
	ENSG00000286746	ENST00000661648.1		n.30+20125C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43510 AN: 151916 Hom.: 7325 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.286 AC: 43518 AN: 152038 Hom.: 7324 Cov.: 32 AF XY: 0.295 AC XY: 21909 AN XY: 74306

African (AFR) AF: 0.128 AC: 5299 AN: 41484

American (AMR) AF: 0.276 AC: 4224 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1234 AN: 3472

East Asian (EAS) AF: 0.232 AC: 1196 AN: 5154

South Asian (SAS) AF: 0.299 AC: 1442 AN: 4828

European-Finnish (FIN) AF: 0.537 AC: 5664 AN: 10542

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23470 AN: 67962

Other (OTH) AF: 0.336 AC: 710 AN: 2110

Alfa AF: 0.337 Hom.: 13610

Bravo AF: 0.260

Asia WGS AF: 0.257 AC: 892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.098
DANN	Benign	0.22
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs11616409; hg19: chr13-81571690;