rs10785303

chr12-41860412-A-G

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, non coding transcript 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: ENST00000550874.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000550874.1	n.472-30487T>C		intron_variant, non_coding_transcript_variant		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;