13-80783536-G-A

Variant names:

• chr13-80783536-G-A
• rs11149178
• ENST00000665186.1:n.151+35375C>T

Variant summary

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

The ENST00000665186.1(ENSG00000286746):​n.151+35375C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,918 control chromosomes in the GnomAD database, including 7,204 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 0.28 (7204 hom., cov: 32)
• Consequence: ENSG00000286746 ENST00000665186.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 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
ENSG00000286746	ENST00000665186.1	n.151+35375C>T		intron_variant	Intron 2 of 4
ENSG00000286746	ENST00000756377.1	n.148+35375C>T		intron_variant	Intron 2 of 3
ENSG00000286746	ENST00000756378.1	n.141-29562C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42952 AN: 151800 Hom.: 7213 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.283 AC: 42935 AN: 151918 Hom.: 7204 Cov.: 32 AF XY: 0.286 AC XY: 21267 AN XY: 74248

African (AFR) AF: 0.115 AC: 4784 AN: 41518

American (AMR) AF: 0.256 AC: 3903 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1031 AN: 3466

East Asian (EAS) AF: 0.277 AC: 1424 AN: 5146

South Asian (SAS) AF: 0.293 AC: 1411 AN: 4814

European-Finnish (FIN) AF: 0.454 AC: 4790 AN: 10546

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.362 AC: 24595 AN: 67882

Other (OTH) AF: 0.321 AC: 675 AN: 2106

Alfa AF: 0.257 Hom.: 2815

Bravo AF: 0.260

Asia WGS AF: 0.265 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0050
DANN	Benign	0.61
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs11149178; hg19: chr13-81357671;