rs10777317

Variant names:

• chr12-91586597-T-C
• rs10777317
• ENST00000685093.1:n.503+47128A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-91586597-T-C
• chr12-91586597-T-G

Variant summary

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

The ENST00000685093.1(ENSG00000289605):​n.503+47128A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,030 control chromosomes in the GnomAD database, including 12,351 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 0.40 (12351 hom., cov: 32)
• Consequence: ENSG00000289605 ENST00000685093.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555
• Publications: 8 publications found

Genes affected

ENSG00000289605 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369896	XR_001749251.2	n.3670+47128A>G		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289605	ENST00000685093.1	n.503+47128A>G		intron_variant	Intron 1 of 9
ENSG00000289605	ENST00000834583.1	n.515+47128A>G		intron_variant	Intron 1 of 2
ENSG00000289605	ENST00000834584.1	n.343+570A>G		intron_variant	Intron 2 of 3
ENSG00000289605	ENST00000834585.1	n.227+47128A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60374 AN: 151912 Hom.: 12336 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.398 AC: 60432 AN: 152030 Hom.: 12351 Cov.: 32 AF XY: 0.398 AC XY: 29551 AN XY: 74328

African (AFR) AF: 0.331 AC: 13725 AN: 41514

American (AMR) AF: 0.499 AC: 7612 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1297 AN: 3466

East Asian (EAS) AF: 0.614 AC: 3177 AN: 5172

South Asian (SAS) AF: 0.455 AC: 2191 AN: 4820

European-Finnish (FIN) AF: 0.354 AC: 3749 AN: 10584

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27354 AN: 67932

Other (OTH) AF: 0.421 AC: 885 AN: 2102

Alfa AF: 0.406 Hom.: 38492

Bravo AF: 0.409

Asia WGS AF: 0.566 AC: 1966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.6
DANN	Benign	0.76
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs10777317; hg19: chr12-91980374;