ENST00000648514.1:n.827+15383T>G

Variant names:

• chr13-80031651-A-C
• rs7995973
• ENST00000648514.1:n.827+15383T>G

Variant summary

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

The ENST00000648514.1(ENSG00000284196):​n.827+15383T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,962 control chromosomes in the GnomAD database, including 8,707 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 0.33 (8707 hom., cov: 32)
• Consequence: ENSG00000284196 ENST00000648514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.49

Genes affected

ENSG00000284196 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 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
ENSG00000284196	ENST00000648514.1	n.827+15383T>G		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50777 AN: 151844 Hom.: 8699 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.334 AC: 50821 AN: 151962 Hom.: 8707 Cov.: 32 AF XY: 0.333 AC XY: 24692 AN XY: 74244

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.353

Alfa AF: 0.333 Hom.: 4630

Bravo AF: 0.332

Asia WGS AF: 0.347 AC: 1210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	13
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7995973; hg19: chr13-80605786;