18-27587981-T-C

Variant names:

• chr18-27587981-T-C
• rs1420956
• ENST00000580883.1:n.253+4727A>G

Variant summary

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

The ENST00000580883.1(ENSG00000264151):​n.253+4727A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,990 control chromosomes in the GnomAD database, including 23,092 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 0.55 (23092 hom., cov: 32)
• Consequence: ENSG00000264151 ENST00000580883.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14
• Publications: 7 publications found

Genes affected

ENSG00000264151 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985126	XR_001753533.1	n.247+4842A>G		intron_variant	Intron 2 of 3
LOC107985126	XR_001753534.2	n.247+4842A>G		intron_variant	Intron 2 of 3
LOC107985126	XR_001753535.1	n.196-5966A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000264151	ENST00000580883.1	n.253+4727A>G		intron_variant	Intron 2 of 3	2
ENSG00000264151	ENST00000584546.5	n.216-5966A>G		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82843 AN: 151872 Hom.: 23058 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.546 AC: 82936 AN: 151990 Hom.: 23092 Cov.: 32 AF XY: 0.545 AC XY: 40484 AN XY: 74280

African (AFR) AF: 0.608 AC: 25207 AN: 41464

American (AMR) AF: 0.624 AC: 9536 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1717 AN: 3470

East Asian (EAS) AF: 0.649 AC: 3342 AN: 5148

South Asian (SAS) AF: 0.563 AC: 2715 AN: 4822

European-Finnish (FIN) AF: 0.443 AC: 4672 AN: 10540

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.500 AC: 33971 AN: 67958

Other (OTH) AF: 0.543 AC: 1143 AN: 2106

Alfa AF: 0.522 Hom.: 62687

Bravo AF: 0.564

Asia WGS AF: 0.611 AC: 2129 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.064
DANN	Benign	0.49
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1420956; hg19: chr18-25167945;