chr18-55762468-T-C

Variant names:

• chr18-55762468-T-C
• rs1642295
• ENST00000587346.1:n.401-77T>C

Variant summary

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

The ENST00000587346.1(ENSG00000267284):​n.401-77T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,206 control chromosomes in the GnomAD database, including 1,389 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 0.10 (1389 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000267284 ENST00000587346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 1 publications found

Genes affected

ENSG00000267284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000587346.1. 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
	ENSG00000267284	ENST00000587346.1	TSL:4	n.401-77T>C		intron	N/A
	ENSG00000267284	ENST00000589662.1	TSL:5	n.218-22431T>C		intron	N/A
	ENSG00000267284	ENST00000654829.1		n.157-22431T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15367 AN: 152088 Hom.: 1387 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0429

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0517

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.0789

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

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) AF: 0.00 AC: 0 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.101 AC: 15383 AN: 152206 Hom.: 1389 Cov.: 32 AF XY: 0.102 AC XY: 7607 AN XY: 74418

African (AFR) AF: 0.200 AC: 8283 AN: 41508

American (AMR) AF: 0.0428 AC: 655 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0236 AC: 82 AN: 3472

East Asian (EAS) AF: 0.378 AC: 1955 AN: 5172

South Asian (SAS) AF: 0.175 AC: 844 AN: 4818

European-Finnish (FIN) AF: 0.0517 AC: 548 AN: 10606

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

European-Non Finnish (NFE) AF: 0.0413 AC: 2807 AN: 68012

Other (OTH) AF: 0.0795 AC: 168 AN: 2114

Alfa AF: 0.0773 Hom.: 101

Bravo AF: 0.104

Asia WGS AF: 0.232 AC: 809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.85
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1642295; hg19: chr18-53429699;