rs1983380

Variant names:

• chr3-118485983-T-A
• rs1983380
• ENST00000482142.5:n.232+10640A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-118485983-T-A
• chr3-118485983-T-C
• chr3-118485983-T-G

Variant summary

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

The ENST00000482142.5(ENSG00000243276):​n.232+10640A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,862 control chromosomes in the GnomAD database, including 16,799 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 0.46 (16799 hom., cov: 31)
• Consequence: ENSG00000243276 ENST00000482142.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425

Genes affected

ENSG00000243276 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.657 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+10640A>T		intron_variant	Intron 3 of 6	5

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69882 AN: 151744 Hom.: 16794 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.460 AC: 69915 AN: 151862 Hom.: 16799 Cov.: 31 AF XY: 0.466 AC XY: 34583 AN XY: 74208

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.513

Alfa AF: 0.327 Hom.: 864

Bravo AF: 0.453

Asia WGS AF: 0.627 AC: 2182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.7
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1983380; hg19: chr3-118204830;