rs9470367

Variant names:

• chr6-36659155-G-C
• rs9470367
• ENST00000778909.1:n.192+1526C>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+1526C>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 152,046 control chromosomes in the GnomAD database, including 9,648 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 (9648 hom., cov: 32)
• Consequence: ENSG00000301446 ENST00000778909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 6 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+1526C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49578 AN: 151928 Hom.: 9651 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.486

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: 49571 AN: 152046 Hom.: 9648 Cov.: 32 AF XY: 0.327 AC XY: 24258 AN XY: 74292

African (AFR) AF: 0.121 AC: 5003 AN: 41484

American (AMR) AF: 0.291 AC: 4437 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1025 AN: 3470

East Asian (EAS) AF: 0.272 AC: 1408 AN: 5178

South Asian (SAS) AF: 0.335 AC: 1615 AN: 4818

European-Finnish (FIN) AF: 0.486 AC: 5123 AN: 10546

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

European-Non Finnish (NFE) AF: 0.439 AC: 29834 AN: 67968

Other (OTH) AF: 0.286 AC: 604 AN: 2112

Alfa AF: 0.379 Hom.: 1507

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	1.4
DANN	Benign	0.70
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs9470367; hg19: chr6-36626932;