rs12686399

Variant names:

• chr9-29393361-A-C
• rs12686399
• ENST00000775037.1:n.254+57028T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-29393361-A-C
• chr9-29393361-A-G
• chr9-29393361-A-T

Variant summary

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

The ENST00000775037.1(ENSG00000300910):​n.254+57028T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 151,888 control chromosomes in the GnomAD database, including 7,047 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 0.30 (7047 hom., cov: 31)
• Consequence: ENSG00000300910 ENST00000775037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 1 publications found

Genes affected

ENSG00000300910 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 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
ENSG00000300910	ENST00000775037.1	n.254+57028T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45297 AN: 151772 Hom.: 7050 Cov.: 31

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.298 AC: 45303 AN: 151888 Hom.: 7047 Cov.: 31 AF XY: 0.305 AC XY: 22612 AN XY: 74236

African (AFR) AF: 0.296 AC: 12280 AN: 41428

American (AMR) AF: 0.340 AC: 5195 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1130 AN: 3468

East Asian (EAS) AF: 0.628 AC: 3227 AN: 5136

South Asian (SAS) AF: 0.355 AC: 1707 AN: 4812

European-Finnish (FIN) AF: 0.293 AC: 3091 AN: 10538

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17837 AN: 67932

Other (OTH) AF: 0.298 AC: 629 AN: 2108

Alfa AF: 0.279 Hom.: 19055

Bravo AF: 0.305

Asia WGS AF: 0.449 AC: 1560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.53
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs12686399; hg19: chr9-29393359; COSMIC: COSV60347960;