13-80133294-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000647704.1(ENSG00000285684):n.390+685T>C variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.301 in 152,148 control chromosomes in the GnomAD database, including 6,957 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 0.30 (6957 hom., cov: 33)
• Consequence: ENST00000647704.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.86

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370275	XR_942116.3	n.189-11418T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000647704.1	n.390+685T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45706 AN: 152030 Hom.: 6944 Cov.: 33

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.301 AC: 45754 AN: 152148 Hom.: 6957 Cov.: 33 AF XY: 0.299 AC XY: 22257 AN XY: 74374

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.292

Alfa AF: 0.284 Hom.: 10859

Bravo AF: 0.314

Asia WGS AF: 0.234 AC: 814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
Cadd	Benign	18
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1215468; hg19: chr13-80707429;