chr13-80997555-G-A

Position:

• chr13-80997555-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000665186.1(ENSG00000286746):​n.58+20125C>T variant causes a intron, non coding transcript 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: ENST00000665186.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000665186.1	n.58+20125C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.336

Alfa AF: 0.341 Hom.: 11539

Bravo AF: 0.260

Asia WGS AF: 0.257 AC: 892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11616409; hg19: chr13-81571690;