16-76927950-G-A

Position:

• chr16-76927950-G-A

Variant summary

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

The ENST00000567777.1(ENSG00000259995):​n.247G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,984 control chromosomes in the GnomAD database, including 10,921 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 (10921 hom., cov: 32)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: ENST00000567777.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000567777.1	n.247G>A		non_coding_transcript_exon_variant	3/3	3

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53832 AN: 151860 Hom.: 10905 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.372

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

Gnomad4 SAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.354 AC: 53876 AN: 151978 Hom.: 10921 Cov.: 32 AF XY: 0.350 AC XY: 26027 AN XY: 74294

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.378

Alfa AF: 0.404 Hom.: 6915

Bravo AF: 0.336

Asia WGS AF: 0.322 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3736338; hg19: chr16-76961847;