rs10514168

Variant names:

• chr18-75386994-C-A
• rs10514168
• ENST00000612669.1:n.-62C>A

Variant summary

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

The ENST00000612669.1(ENSG00000276993):​n.-62C>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,296 control chromosomes in the GnomAD database, including 1,394 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 (1394 hom., cov: 33)
  • Exomes 𝑓: 0.14 (0 hom.)
• Consequence: ENSG00000276993 ENST00000612669.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.813

Genes affected

ENSG00000276993 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.158 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
ENSG00000276993	ENST00000612669.1	n.-62C>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19520 AN: 152158 Hom.: 1391 Cov.: 33

Gnomad AFR AF: 0.0721

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.00788

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.125

GnomAD4 exome AF: 0.136 AC: 3 AN: 22 Hom.: 0 AF XY: 0.125 AC XY: 2 AN XY: 16

Gnomad4 FIN exome AF: 0.100

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.128 AC: 19547 AN: 152274 Hom.: 1394 Cov.: 33 AF XY: 0.125 AC XY: 9316 AN XY: 74464

Gnomad4 AFR AF: 0.0722

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.0893

Gnomad4 EAS AF: 0.00790

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.124

Alfa AF: 0.143 Hom.: 223

Bravo AF: 0.129

Asia WGS AF: 0.0730 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	4.1
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514168; hg19: chr18-73098949;