rs1560104

Variant names:

• chr16-12614351-C-T
• rs1560104
• ENST00000615100.1:n.-100C>T

Variant summary

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

The ENST00000615100.1(ENSG00000274834):​n.-100C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,910 control chromosomes in the GnomAD database, including 15,637 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 0.43 (15637 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000274834 ENST00000615100.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

Genes affected

ENSG00000274834 (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 (EAS) allele frequency at 95% confidence interval = 0.666 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
ENSG00000274834	ENST00000615100.1	n.-100C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64985 AN: 151790 Hom.: 15614 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.409

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

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.428 AC: 65059 AN: 151908 Hom.: 15637 Cov.: 32 AF XY: 0.427 AC XY: 31682 AN XY: 74192

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.411

Alfa AF: 0.412 Hom.: 1350

Bravo AF: 0.451

Asia WGS AF: 0.567 AC: 1969 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	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1560104; hg19: chr16-12708208;