rs10783746

Variant names:

• chr12-55467246-G-A
• rs10783746
• ENST00000554049.1:n.142+9303C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-55467246-G-A
• chr12-55467246-G-C

Variant summary

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

The ENST00000554049.1(ENSG00000258763):​n.142+9303C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,934 control chromosomes in the GnomAD database, including 9,016 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 0.33 (9016 hom., cov: 32)
• Consequence: ENSG00000258763 ENST00000554049.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468

Genes affected

ENSG00000258763 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.393 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
ENSG00000258763	ENST00000554049.1	n.142+9303C>T		intron_variant	Intron 2 of 2	2
ENSG00000258763	ENST00000555138.1	n.125+25845C>T		intron_variant	Intron 2 of 2	2
ENSG00000258763	ENST00000555146.5	n.137+9303C>T		intron_variant	Intron 2 of 2	3
ENSG00000258763	ENST00000556750.5	n.178+9303C>T		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50440 AN: 151816 Hom.: 9013 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.332 AC: 50443 AN: 151934 Hom.: 9016 Cov.: 32 AF XY: 0.336 AC XY: 24956 AN XY: 74254

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.366

Alfa AF: 0.378 Hom.: 15227

Bravo AF: 0.326

Asia WGS AF: 0.344 AC: 1198 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	5.8
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10783746; hg19: chr12-55861030;