16-31711093-C-T

Position:

• chr16-31711093-C-T

Variant summary

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

The ENST00000562354.2(ENSG00000290927):​n.3224C>T 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 0.128 in 152,120 control chromosomes in the GnomAD database, including 1,596 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 0.13 (1595 hom., cov: 32)
  • Exomes 𝑓: 0.10 (1 hom.)
• Consequence: ENSG00000290927 ENST00000562354.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

Genes affected

ENSG00000290927 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31711093C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290927	ENST00000562354.2	n.3224C>T		non_coding_transcript_exon_variant	2/2	1
ENSG00000261731	ENST00000569175.2	n.240+652G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19372 AN: 151924 Hom.: 1592 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0242

Gnomad AMR AF: 0.0878

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0755

Gnomad OTH AF: 0.120

GnomAD4 exome AF: 0.103 AC: 8 AN: 78 Hom.: 1 Cov.: 0 AF XY: 0.0962 AC XY: 5 AN XY: 52

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.0781

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.128 AC: 19390 AN: 152042 Hom.: 1595 Cov.: 32 AF XY: 0.133 AC XY: 9849 AN XY: 74314

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.0876

Gnomad4 ASJ AF: 0.0533

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.0755

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0488 Hom.: 50

Bravo AF: 0.122

Asia WGS AF: 0.292 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17839519; hg19: chr16-31722414;