chr18-57316323-G-T

Variant names:

• chr18-57316323-G-T
• rs1120787
• ENST00000718553.1:n.61-62030C>A

Variant summary

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

The ENST00000718553.1(ENSG00000293721):​n.61-62030C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,026 control chromosomes in the GnomAD database, including 4,469 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 0.18 (4469 hom., cov: 33)
• Consequence: ENSG00000293721 ENST00000718553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.857
• Publications: 6 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=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 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
ENSG00000293721	ENST00000718553.1	n.61-62030C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27683 AN: 151908 Hom.: 4434 Cov.: 33

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0508

Gnomad EAS AF: 0.0730

Gnomad SAS AF: 0.0408

Gnomad FIN AF: 0.0984

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0821

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.183 AC: 27780 AN: 152026 Hom.: 4469 Cov.: 33 AF XY: 0.177 AC XY: 13175 AN XY: 74338

African (AFR) AF: 0.440 AC: 18262 AN: 41466

American (AMR) AF: 0.110 AC: 1681 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0508 AC: 176 AN: 3464

East Asian (EAS) AF: 0.0728 AC: 377 AN: 5182

South Asian (SAS) AF: 0.0414 AC: 200 AN: 4830

European-Finnish (FIN) AF: 0.0984 AC: 1039 AN: 10560

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0821 AC: 5575 AN: 67922

Other (OTH) AF: 0.148 AC: 312 AN: 2108

Alfa AF: 0.139 Hom.: 3259

Bravo AF: 0.196

Asia WGS AF: 0.0810 AC: 281 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.33
DANN	Benign	0.22
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs1120787; hg19: chr18-54983554;