rs933890

Variant names:

• chr12-108045145-T-C
• rs933890
• ENST00000787792.1:n.88+1032A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000787792.1(ENSG00000302551):​n.88+1032A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,252 control chromosomes in the GnomAD database, including 1,929 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 (1929 hom., cov: 32)
• Consequence: ENSG00000302551 ENST00000787792.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.862
• Publications: 4 publications found

Genes affected

ENSG00000302551 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 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
ENSG00000302551	ENST00000787792.1	n.88+1032A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21651 AN: 152134 Hom.: 1928 Cov.: 32

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0518

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.142 AC: 21653 AN: 152252 Hom.: 1929 Cov.: 32 AF XY: 0.136 AC XY: 10100 AN XY: 74444

African (AFR) AF: 0.0700 AC: 2908 AN: 41534

American (AMR) AF: 0.153 AC: 2335 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5188

South Asian (SAS) AF: 0.0525 AC: 253 AN: 4822

European-Finnish (FIN) AF: 0.130 AC: 1375 AN: 10612

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13617 AN: 68008

Other (OTH) AF: 0.159 AC: 335 AN: 2112

Alfa AF: 0.163 Hom.: 357

Bravo AF: 0.145

Asia WGS AF: 0.0330 AC: 117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	18
DANN	Benign	0.80
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs933890; hg19: chr12-108438922;