rs13330107

chr16-76844965-G-A

Variant summary

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

The ENST00000567777.1(ENSG00000259995):n.139-67390G>A 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 0.352 in 151,982 control chromosomes in the GnomAD database, including 9,523 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 0.35 (9523 hom., cov: 32)
• Consequence: ENST00000567777.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 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
	ENST00000567777.1	n.139-67390G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53528 AN: 151864 Hom.: 9514 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.352 AC: 53567 AN: 151982 Hom.: 9523 Cov.: 32 AF XY: 0.345 AC XY: 25598 AN XY: 74290

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.370

Alfa AF: 0.366 Hom.: 18592

Bravo AF: 0.354

Asia WGS AF: 0.350 AC: 1219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.50
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13330107; hg19: chr16-76878862;