ENST00000612669.1:n.-62C>A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000276993 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.100 AC: 1 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.200 AC: 2 AN: 10

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.0722 AC: 3000 AN: 41554

American (AMR) AF: 0.163 AC: 2495 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0893 AC: 310 AN: 3470

East Asian (EAS) AF: 0.00790 AC: 41 AN: 5192

South Asian (SAS) AF: 0.106 AC: 512 AN: 4826

European-Finnish (FIN) AF: 0.162 AC: 1721 AN: 10606

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.161 AC: 10948 AN: 68012

Other (OTH) AF: 0.124 AC: 263 AN: 2116

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
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs10514168; hg19: chr18-73098949;