rs10809674

Variant names:

• chr9-12015741-G-A
• rs10809674
• ENST00000649122.1:n.389-40474G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649122.1(ENSG00000285784):​n.389-40474G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,760 control chromosomes in the GnomAD database, including 9,943 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 (9943 hom., cov: 32)
• Consequence: ENSG00000285784 ENST00000649122.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

Genes affected

ENSG00000285784 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 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
ENSG00000285784	ENST00000649122.1	n.389-40474G>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49802 AN: 151640 Hom.: 9948 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.328 AC: 49796 AN: 151760 Hom.: 9943 Cov.: 32 AF XY: 0.326 AC XY: 24141 AN XY: 74156

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.335

Alfa AF: 0.397 Hom.: 8857

Bravo AF: 0.307

Asia WGS AF: 0.332 AC: 1154 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10809674; hg19: chr9-12015741; COSMIC: COSV69447714;