chr10-267564-C-T

Variant names:

• chr10-267564-C-T
• rs4880568
• XR_007062029.1:n.1328+3228G>A

Variant summary

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

The XR_007062029.1(LOC107984191):​n.1328+3228G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 152,002 control chromosomes in the GnomAD database, including 26,449 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 0.59 (26449 hom., cov: 32)
• Consequence: LOC107984191 XR_007062029.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 6 publications found

Genes affected

LOC107984191 (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 = 0.636 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88979 AN: 151884 Hom.: 26434 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.586 AC: 89023 AN: 152002 Hom.: 26449 Cov.: 32 AF XY: 0.581 AC XY: 43135 AN XY: 74298

African (AFR) AF: 0.540 AC: 22368 AN: 41448

American (AMR) AF: 0.547 AC: 8339 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2087 AN: 3464

East Asian (EAS) AF: 0.370 AC: 1906 AN: 5156

South Asian (SAS) AF: 0.592 AC: 2851 AN: 4814

European-Finnish (FIN) AF: 0.543 AC: 5737 AN: 10570

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43559 AN: 67974

Other (OTH) AF: 0.616 AC: 1300 AN: 2112

Alfa AF: 0.619 Hom.: 113285

Bravo AF: 0.578

Asia WGS AF: 0.501 AC: 1745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.069
DANN	Benign	0.79
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4880568; hg19: chr10-313504;