rs9368950

Variant names:

• chr6-36660095-T-C
• rs9368950
• ENST00000778909.1:n.192+586A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-36660095-T-C
• chr6-36660095-T-G

Variant summary

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

The ENST00000778909.1(ENSG00000301446):​n.192+586A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,226 control chromosomes in the GnomAD database, including 9,633 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 0.33 (9633 hom., cov: 33)
• Consequence: ENSG00000301446 ENST00000778909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 14 publications found

Genes affected

ENSG00000301446 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 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
ENSG00000301446	ENST00000778909.1	n.192+586A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49561 AN: 152108 Hom.: 9636 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.326 AC: 49555 AN: 152226 Hom.: 9633 Cov.: 33 AF XY: 0.326 AC XY: 24258 AN XY: 74426

African (AFR) AF: 0.121 AC: 5023 AN: 41550

American (AMR) AF: 0.287 AC: 4391 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1024 AN: 3472

East Asian (EAS) AF: 0.272 AC: 1409 AN: 5176

South Asian (SAS) AF: 0.334 AC: 1614 AN: 4826

European-Finnish (FIN) AF: 0.485 AC: 5139 AN: 10594

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29829 AN: 67992

Other (OTH) AF: 0.286 AC: 604 AN: 2114

Alfa AF: 0.386 Hom.: 37501

Bravo AF: 0.300

Asia WGS AF: 0.274 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.44
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9368950; hg19: chr6-36627872;