rs10506789

Variant names:

• chr12-78736853-C-G
• rs10506789
• ENST00000799436.1:n.292+4036C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000799436.1(ENSG00000257948):​n.292+4036C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00795 in 152,114 control chromosomes in the GnomAD database, including 26 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 0.0079 (26 hom., cov: 32)
• Consequence: ENSG00000257948 ENST00000799436.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 0 publications found

Genes affected

ENSG00000257948 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.073 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
ENSG00000257948	ENST00000799436.1	n.292+4036C>G		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.00795 AC: 1208 AN: 151996 Hom.: 26 Cov.: 32

Gnomad AFR AF: 0.00162

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0119

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.0792

Gnomad SAS AF: 0.00498

Gnomad FIN AF: 0.00264

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00638

Gnomad OTH AF: 0.00670

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

GnomAD4 genome AF: 0.00795 AC: 1209 AN: 152114 Hom.: 26 Cov.: 32 AF XY: 0.00817 AC XY: 607 AN XY: 74340

African (AFR) AF: 0.00161 AC: 67 AN: 41502

American (AMR) AF: 0.0119 AC: 182 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 49 AN: 3468

East Asian (EAS) AF: 0.0794 AC: 410 AN: 5166

South Asian (SAS) AF: 0.00499 AC: 24 AN: 4814

European-Finnish (FIN) AF: 0.00264 AC: 28 AN: 10598

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00638 AC: 434 AN: 67982

Other (OTH) AF: 0.00664 AC: 14 AN: 2110

Alfa AF: 0.00688 Hom.: 2

Bravo AF: 0.00971

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.70
DANN	Benign	0.33
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs10506789; hg19: chr12-79130633;