rs10785303

Variant names:

• chr12-41860412-A-G
• rs10785303
• ENST00000550874.1:n.472-30487T>C

Variant summary

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

The ENST00000550874.1(ENSG00000257239):​n.472-30487T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,206 control chromosomes in the GnomAD database, including 1,520 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 0.14 (1520 hom., cov: 32)
• Consequence: ENSG00000257239 ENST00000550874.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

Genes affected

ENSG00000257239 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.164 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
ENSG00000257239	ENST00000550874.1	n.472-30487T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21520 AN: 152088 Hom.: 1518 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.141 AC: 21523 AN: 152206 Hom.: 1520 Cov.: 32 AF XY: 0.142 AC XY: 10598 AN XY: 74420

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.134

Alfa AF: 0.141 Hom.: 933

Bravo AF: 0.141

Asia WGS AF: 0.148 AC: 514 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10785303; hg19: chr12-42254214;