rs500097

chr3-118395843-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000482142.5(ENSG00000243276):n.232+100780G>A variant causes a intron, non coding transcript 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: ENST00000482142.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000482142.5	n.232+100780G>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.903

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.815

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.739

Alfa AF: 0.714 Hom.: 21248

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs500097; hg19: chr3-118114690;