ENST00000657542.1:n.528-7114T>G

Variant names:

• chr18-30405513-T-G
• rs4799964
• ENST00000657542.1:n.528-7114T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657542.1(ENSG00000286605):​n.528-7114T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0304 in 152,296 control chromosomes in the GnomAD database, including 91 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 0.030 (91 hom., cov: 33)
• Consequence: ENSG00000286605 ENST00000657542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255

Genes affected

ENSG00000286605 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0797 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
ENSG00000286605	ENST00000657542.1	n.528-7114T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0304 AC: 4629 AN: 152178 Hom.: 92 Cov.: 33

Gnomad AFR AF: 0.0144

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0484

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.0865

Gnomad SAS AF: 0.0546

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0313

Gnomad OTH AF: 0.0401

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

GnomAD4 genome AF: 0.0304 AC: 4623 AN: 152296 Hom.: 91 Cov.: 33 AF XY: 0.0306 AC XY: 2281 AN XY: 74462

Gnomad4 AFR AF: 0.0143

Gnomad4 AMR AF: 0.0483

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.0863

Gnomad4 SAS AF: 0.0543

Gnomad4 FIN AF: 0.0238

Gnomad4 NFE AF: 0.0313

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.00961 Hom.: 3

Bravo AF: 0.0322

Asia WGS AF: 0.0880 AC: 306 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4799964; hg19: chr18-27985479;