rs1482108

Variant names:

• chr4-52261891-G-A
• rs1482108
• ENST00000660768.1:n.204-8547C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-52261891-G-A
• chr4-52261891-G-C
• chr4-52261891-G-T

Variant summary

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

The ENST00000660768.1(ENSG00000287999):​n.204-8547C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 151,968 control chromosomes in the GnomAD database, including 41,388 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 0.73 (41388 hom., cov: 32)
• Consequence: ENSG00000287999 ENST00000660768.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332
• Publications: 2 publications found

Genes affected

ENSG00000287999 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 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
ENSG00000287999	ENST00000660768.1	n.204-8547C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111014 AN: 151850 Hom.: 41358 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.731 AC: 111098 AN: 151968 Hom.: 41388 Cov.: 32 AF XY: 0.733 AC XY: 54466 AN XY: 74284

African (AFR) AF: 0.577 AC: 23873 AN: 41404

American (AMR) AF: 0.815 AC: 12449 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2447 AN: 3472

East Asian (EAS) AF: 0.915 AC: 4714 AN: 5154

South Asian (SAS) AF: 0.756 AC: 3633 AN: 4804

European-Finnish (FIN) AF: 0.759 AC: 8022 AN: 10572

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.784 AC: 53296 AN: 67968

Other (OTH) AF: 0.766 AC: 1616 AN: 2110

Alfa AF: 0.760 Hom.: 7482

Bravo AF: 0.728

Asia WGS AF: 0.829 AC: 2884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.36
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1482108; hg19: chr4-53128057;