rs4996482

Variant names:

• chr18-55787138-C-A
• rs4996482
• ENST00000589662.1:n.364+482C>A

Variant summary

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

The ENST00000589662.1(ENSG00000267284):​n.364+482C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,086 control chromosomes in the GnomAD database, including 5,827 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 0.26 (5827 hom., cov: 32)
• Consequence: ENSG00000267284 ENST00000589662.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 5 publications found

Genes affected

ENSG00000267284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372130	XR_007066382.1	n.475+482C>A		intron_variant	Intron 4 of 8
LOC105372130	XR_007066383.1	n.1171-1475C>A		intron_variant	Intron 1 of 4
LOC105372130	XR_935487.3	n.1241+482C>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267284	ENST00000589662.1	n.364+482C>A		intron_variant	Intron 3 of 3	5
ENSG00000267284	ENST00000654829.1	n.303+482C>A		intron_variant	Intron 4 of 8
ENSG00000267284	ENST00000729561.1	n.547+482C>A		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39953 AN: 151968 Hom.: 5821 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.263 AC: 39998 AN: 152086 Hom.: 5827 Cov.: 32 AF XY: 0.263 AC XY: 19518 AN XY: 74330

African (AFR) AF: 0.142 AC: 5904 AN: 41498

American (AMR) AF: 0.384 AC: 5857 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3472

East Asian (EAS) AF: 0.178 AC: 919 AN: 5168

South Asian (SAS) AF: 0.175 AC: 844 AN: 4818

European-Finnish (FIN) AF: 0.274 AC: 2900 AN: 10566

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21744 AN: 67980

Other (OTH) AF: 0.267 AC: 565 AN: 2114

Alfa AF: 0.304 Hom.: 20133

Bravo AF: 0.267

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	4.6
DANN	Benign	0.83
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs4996482; hg19: chr18-53454369;