rs1870481

Variant names:

• chr4-117741865-C-T
• rs1870481
• ENST00000755294.1:n.275+7448G>A

Variant summary

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

The ENST00000755294.1(ENSG00000288921):​n.275+7448G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 152,044 control chromosomes in the GnomAD database, including 24,269 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 0.54 (24269 hom., cov: 33)
• Consequence: ENSG00000288921 ENST00000755294.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 8 publications found

Genes affected

ENSG00000288921 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 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
ENSG00000288921	ENST00000755294.1	n.275+7448G>A		intron_variant	Intron 3 of 5
ENSG00000288921	ENST00000755295.1	n.350+7349G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82544 AN: 151926 Hom.: 24228 Cov.: 33

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.544 AC: 82644 AN: 152044 Hom.: 24269 Cov.: 33 AF XY: 0.542 AC XY: 40276 AN XY: 74312

African (AFR) AF: 0.783 AC: 32505 AN: 41510

American (AMR) AF: 0.540 AC: 8235 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1733 AN: 3468

East Asian (EAS) AF: 0.595 AC: 3067 AN: 5152

South Asian (SAS) AF: 0.428 AC: 2068 AN: 4830

European-Finnish (FIN) AF: 0.405 AC: 4275 AN: 10562

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.424 AC: 28849 AN: 67962

Other (OTH) AF: 0.552 AC: 1167 AN: 2114

Alfa AF: 0.483 Hom.: 9763

Bravo AF: 0.569

Asia WGS AF: 0.517 AC: 1794 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.31
DANN	Benign	0.83
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1870481; hg19: chr4-118663020;