rs1371264

Variant names:

• chr18-1775083-A-G
• rs1371264
• ENST00000580524.1:n.409-4776A>G

Variant summary

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

The ENST00000580524.1(ENSG00000266602):​n.409-4776A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 152,022 control chromosomes in the GnomAD database, including 34,588 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 0.67 (34588 hom., cov: 32)
• Consequence: ENSG00000266602 ENST00000580524.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 7 publications found

Genes affected

ENSG00000266602 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 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
ENSG00000266602	ENST00000580524.1	n.409-4776A>G		intron_variant	Intron 2 of 2	3
ENSG00000266602	ENST00000653094.1	n.326-49695A>G		intron_variant	Intron 3 of 5
ENSG00000266602	ENST00000653330.1	n.252-49695A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101308 AN: 151904 Hom.: 34573 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.667 AC: 101359 AN: 152022 Hom.: 34588 Cov.: 32 AF XY: 0.669 AC XY: 49691 AN XY: 74308

African (AFR) AF: 0.513 AC: 21286 AN: 41470

American (AMR) AF: 0.667 AC: 10177 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2727 AN: 3462

East Asian (EAS) AF: 0.737 AC: 3813 AN: 5174

South Asian (SAS) AF: 0.687 AC: 3308 AN: 4816

European-Finnish (FIN) AF: 0.783 AC: 8281 AN: 10576

Middle Eastern (MID) AF: 0.750 AC: 219 AN: 292

European-Non Finnish (NFE) AF: 0.729 AC: 49524 AN: 67956

Other (OTH) AF: 0.689 AC: 1454 AN: 2110

Alfa AF: 0.713 Hom.: 28253

Bravo AF: 0.652

Asia WGS AF: 0.676 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.67
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1371264; hg19: chr18-1775084;