3-118402488-G-A

Variant names:

• chr3-118402488-G-A
• rs488628
• ENST00000482142.5:n.232+94135C>T

Variant summary

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

The ENST00000482142.5(ENSG00000243276):​n.232+94135C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 151,700 control chromosomes in the GnomAD database, including 4,841 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 0.25 (4841 hom., cov: 32)
• Consequence: ENSG00000243276 ENST00000482142.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.605
• Publications: 2 publications found

Genes affected

ENSG00000243276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000482142.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000243276	ENST00000482142.5	TSL:5	n.232+94135C>T		intron	N/A
	ENSG00000243276	ENST00000833975.1		n.449-60214C>T		intron	N/A
	ENSG00000243276	ENST00000833976.1		n.350-60214C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37955 AN: 151582 Hom.: 4827 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.0971

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.250 AC: 37998 AN: 151700 Hom.: 4841 Cov.: 32 AF XY: 0.249 AC XY: 18491 AN XY: 74126

African (AFR) AF: 0.290 AC: 12019 AN: 41404

American (AMR) AF: 0.227 AC: 3466 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 843 AN: 3450

East Asian (EAS) AF: 0.271 AC: 1399 AN: 5162

South Asian (SAS) AF: 0.0978 AC: 472 AN: 4828

European-Finnish (FIN) AF: 0.257 AC: 2703 AN: 10528

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16331 AN: 67776

Other (OTH) AF: 0.216 AC: 456 AN: 2108

Alfa AF: 0.243 Hom.: 17523

Bravo AF: 0.253

Asia WGS AF: 0.159 AC: 555 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	8.2
DANN	Benign	0.49
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs488628; hg19: chr3-118121335;