rs4940711

Variant names:

• chr18-58468360-C-T
• rs4940711
• ENST00000735990.1:n.355+7590C>T

Variant summary

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

The ENST00000735990.1(ENSG00000296058):​n.355+7590C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 152,100 control chromosomes in the GnomAD database, including 31,376 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 0.62 (31376 hom., cov: 33)
• Consequence: ENSG00000296058 ENST00000735990.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 1 publications found

Genes affected

ENSG00000296058 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 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
ENSG00000296058	ENST00000735990.1	n.355+7590C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93905 AN: 151982 Hom.: 31373 Cov.: 33

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.617 AC: 93920 AN: 152100 Hom.: 31376 Cov.: 33 AF XY: 0.619 AC XY: 46003 AN XY: 74360

African (AFR) AF: 0.333 AC: 13782 AN: 41446

American (AMR) AF: 0.710 AC: 10853 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2480 AN: 3472

East Asian (EAS) AF: 0.755 AC: 3909 AN: 5176

South Asian (SAS) AF: 0.640 AC: 3080 AN: 4816

European-Finnish (FIN) AF: 0.721 AC: 7633 AN: 10584

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49913 AN: 68006

Other (OTH) AF: 0.643 AC: 1360 AN: 2114

Alfa AF: 0.671 Hom.: 4501

Bravo AF: 0.606

Asia WGS AF: 0.679 AC: 2362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.62
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs4940711; hg19: chr18-56135592;