18-59084822-G-C

Variant names:

• chr18-59084822-G-C
• rs1037757
• ENST00000589729.2:n.511G>C

Variant summary

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

The ENST00000591900.2(ENSG00000267215):​n.889G>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 0.0456 in 152,336 control chromosomes in the GnomAD database, including 370 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 0.046 (370 hom., cov: 32)
  • Exomes 𝑓: 0.0086 (0 hom.)
• Consequence: ENSG00000267215 ENST00000591900.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 8 publications found

Genes affected

ENSG00000267215 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000591900.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267215	ENST00000589729.2	TSL:5	n.511G>C		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000267215	ENST00000591900.2	TSL:4	n.889G>C		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000267215	ENST00000655415.2		n.731G>C		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0456 AC: 6940 AN: 152102 Hom.: 370 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0229

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0153

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0153

Gnomad OTH AF: 0.0388

GnomAD4 exome AF: 0.00862 AC: 1 AN: 116 Hom.: 0 Cov.: 0 AF XY: 0.0147 AC XY: 1 AN XY: 68

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: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00893 AC: 1 AN: 112

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

GnomAD4 genome AF: 0.0457 AC: 6951 AN: 152220 Hom.: 370 Cov.: 32 AF XY: 0.0435 AC XY: 3235 AN XY: 74426

African (AFR) AF: 0.123 AC: 5115 AN: 41508

American (AMR) AF: 0.0229 AC: 350 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0320 AC: 111 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0164 AC: 79 AN: 4822

European-Finnish (FIN) AF: 0.0153 AC: 162 AN: 10610

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0153 AC: 1041 AN: 68012

Other (OTH) AF: 0.0388 AC: 82 AN: 2112

Alfa AF: 0.00379 Hom.: 1

Bravo AF: 0.0515

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.54
DANN	Benign	0.38
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1037757; hg19: chr18-56752054;