rs10735088

Variant names:

• chr12-115586256-T-C
• rs10735088
• ENST00000551531.1:n.177-3291A>G

Variant summary

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

The ENST00000551531.1(ENSG00000257407):​n.177-3291A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 152,132 control chromosomes in the GnomAD database, including 47,250 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 0.79 (47250 hom., cov: 31)
• Consequence: ENSG00000257407 ENST00000551531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97
• Publications: 2 publications found

Genes affected

ENSG00000257407 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370002	NR_188486.1	n.612-3291A>G		intron_variant	Intron 4 of 5
LOC105370002	NR_188487.1	n.537-3291A>G		intron_variant	Intron 4 of 5
LOC105370003	XR_945388.3	n.119-77842A>G		intron_variant	Intron 1 of 3
LOC105370003	XR_945389.3	n.119-77842A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257407	ENST00000551531.1	n.177-3291A>G		intron_variant	Intron 2 of 3	3
ENSG00000257407	ENST00000551940.1	n.344-3291A>G		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119567 AN: 152012 Hom.: 47222 Cov.: 31

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.786 AC: 119641 AN: 152132 Hom.: 47250 Cov.: 31 AF XY: 0.790 AC XY: 58726 AN XY: 74358

African (AFR) AF: 0.720 AC: 29872 AN: 41486

American (AMR) AF: 0.810 AC: 12382 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2673 AN: 3470

East Asian (EAS) AF: 0.922 AC: 4772 AN: 5176

South Asian (SAS) AF: 0.821 AC: 3949 AN: 4812

European-Finnish (FIN) AF: 0.818 AC: 8659 AN: 10584

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.807 AC: 54890 AN: 67998

Other (OTH) AF: 0.787 AC: 1662 AN: 2112

Alfa AF: 0.800 Hom.: 68856

Bravo AF: 0.780

Asia WGS AF: 0.862 AC: 2995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.63
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs10735088; hg19: chr12-116024061;