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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685093.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289605	ENST00000685093.1		n.503+47128A>G		intron	N/A
	ENSG00000289605	ENST00000834583.1		n.515+47128A>G		intron	N/A
	ENSG00000289605	ENST00000834584.1		n.343+570A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10777317;

hg19: chr12-91980374;