18-52338491-C-G

Variant names:

• chr18-52338491-C-G
• rs934345
• ENST00000582700.1:n.535G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000582700.1(ENSG00000266335):​n.535G>C 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 0.632 in 152,124 control chromosomes in the GnomAD database, including 31,393 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 0.63 (31393 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000266335 ENST00000582700.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 5 publications found

Genes affected

ENSG00000266335 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 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
ENSG00000266335	ENST00000582700.1	n.535G>C		non_coding_transcript_exon_variant	Exon 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96034 AN: 152006 Hom.: 31346 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.631

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.632 AC: 96138 AN: 152124 Hom.: 31393 Cov.: 32 AF XY: 0.630 AC XY: 46876 AN XY: 74362

African (AFR) AF: 0.799 AC: 33202 AN: 41530

American (AMR) AF: 0.651 AC: 9947 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2053 AN: 3468

East Asian (EAS) AF: 0.705 AC: 3633 AN: 5156

South Asian (SAS) AF: 0.655 AC: 3161 AN: 4824

European-Finnish (FIN) AF: 0.504 AC: 5336 AN: 10578

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36707 AN: 67968

Other (OTH) AF: 0.631 AC: 1332 AN: 2112

Alfa AF: 0.428 Hom.: 1050

Bravo AF: 0.652

Asia WGS AF: 0.676 AC: 2349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.11
DANN	Benign	0.64
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs934345; hg19: chr18-49864861;