rs500097

Variant names:

• chr3-118395843-C-T
• rs500097
• ENST00000482142.5:n.232+100780G>A

Variant summary

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

The ENST00000482142.5(ENSG00000243276):​n.232+100780G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,134 control chromosomes in the GnomAD database, including 44,481 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 0.76 (44481 hom., cov: 33)
• Consequence: ENSG00000243276 ENST00000482142.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 1 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 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
ENSG00000243276	ENST00000482142.5	n.232+100780G>A		intron_variant	Intron 3 of 6	5
ENSG00000243276	ENST00000833975.1	n.449-53569G>A		intron_variant	Intron 5 of 5
ENSG00000243276	ENST00000833976.1	n.350-53569G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115342 AN: 152016 Hom.: 44437 Cov.: 33

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.759 AC: 115442 AN: 152134 Hom.: 44481 Cov.: 33 AF XY: 0.757 AC XY: 56295 AN XY: 74368

African (AFR) AF: 0.903 AC: 37520 AN: 41536

American (AMR) AF: 0.728 AC: 11131 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2493 AN: 3472

East Asian (EAS) AF: 0.815 AC: 4223 AN: 5182

South Asian (SAS) AF: 0.662 AC: 3193 AN: 4826

European-Finnish (FIN) AF: 0.648 AC: 6833 AN: 10548

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.702 AC: 47727 AN: 67972

Other (OTH) AF: 0.739 AC: 1561 AN: 2112

Alfa AF: 0.716 Hom.: 23555

Bravo AF: 0.772

Asia WGS AF: 0.714 AC: 2486 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	1.1
DANN	Benign	0.60
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs500097; hg19: chr3-118114690;