rs10485409

Variant names:

• chr6-90795693-C-T
• rs10485409
• XR_001744259.1:n.1244-112363C>T

Variant summary

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

The XR_001744259.1(LOC107986623):​n.1244-112363C>T 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 151,906 control chromosomes in the GnomAD database, including 12,151 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 (12151 hom., cov: 32)
• Consequence: LOC107986623 XR_001744259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 3 publications found

Genes affected

LOC107986623 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60388 AN: 151788 Hom.: 12137 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.398 AC: 60454 AN: 151906 Hom.: 12151 Cov.: 32 AF XY: 0.406 AC XY: 30127 AN XY: 74232

African (AFR) AF: 0.448 AC: 18564 AN: 41400

American (AMR) AF: 0.441 AC: 6732 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1361 AN: 3466

East Asian (EAS) AF: 0.466 AC: 2394 AN: 5140

South Asian (SAS) AF: 0.498 AC: 2397 AN: 4814

European-Finnish (FIN) AF: 0.438 AC: 4629 AN: 10578

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23249 AN: 67926

Other (OTH) AF: 0.385 AC: 813 AN: 2112

Alfa AF: 0.359 Hom.: 43717

Bravo AF: 0.395

Asia WGS AF: 0.478 AC: 1663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.63
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs10485409; hg19: chr6-91505411;