18-57399314-A-G

Variant names:

• chr18-57399314-A-G
• rs221877
• ENST00000718553.1:n.60+24562T>C

Variant summary

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

The ENST00000718553.1(ENSG00000293721):​n.60+24562T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,056 control chromosomes in the GnomAD database, including 6,043 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 0.23 (6043 hom., cov: 32)
• Consequence: ENSG00000293721 ENST00000718553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229
• Publications: 3 publications found

Genes affected

ENSG00000293721 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718553.1. 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
	ENSG00000293721	ENST00000718553.1		n.60+24562T>C		intron	N/A
	ENSG00000293721	ENST00000718554.1		n.86+24562T>C		intron	N/A
	ENSG00000293721	ENST00000718555.1		n.48+24562T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35350 AN: 151938 Hom.: 6025 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.181

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.233 AC: 35417 AN: 152056 Hom.: 6043 Cov.: 32 AF XY: 0.230 AC XY: 17117 AN XY: 74366

African (AFR) AF: 0.485 AC: 20065 AN: 41386

American (AMR) AF: 0.166 AC: 2538 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3464

East Asian (EAS) AF: 0.136 AC: 705 AN: 5180

South Asian (SAS) AF: 0.117 AC: 564 AN: 4828

European-Finnish (FIN) AF: 0.152 AC: 1610 AN: 10588

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8806 AN: 68002

Other (OTH) AF: 0.180 AC: 380 AN: 2116

Alfa AF: 0.155 Hom.: 10797

Bravo AF: 0.245

Asia WGS AF: 0.134 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.3
DANN	Benign	0.75
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs221877; hg19: chr18-55066546;