16-13767336-C-T

Position:

• chr16-13767336-C-T

Variant summary

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

The ENST00000573369.5(ENSG00000262267):​n.402G>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 0.549 in 152,078 control chromosomes in the GnomAD database, including 25,513 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 0.55 (25513 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: ENST00000573369.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903645	XR_007064996.1	n.156G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000573369.5	n.402G>A		non_coding_transcript_exon_variant	4/5	5
	ENST00000659657.1	n.35G>A		non_coding_transcript_exon_variant	1/2
	ENST00000576944.1	n.383+10384G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83491 AN: 151956 Hom.: 25529 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.572

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.549 AC: 83484 AN: 152074 Hom.: 25513 Cov.: 32 AF XY: 0.550 AC XY: 40900 AN XY: 74326

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.563

Alfa AF: 0.625 Hom.: 20331

Bravo AF: 0.531

Asia WGS AF: 0.588 AC: 2045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	12
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12599027; hg19: chr16-13861193;