rs10456831

Variant names:

• chr6-18506533-C-T
• rs10456831
• XR_926548.3:n.273-2339C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_926548.3(LOC105374955):​n.273-2339C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0344 in 152,258 control chromosomes in the GnomAD database, including 101 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 0.034 (101 hom., cov: 32)
• Consequence: LOC105374955 XR_926548.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435
• Publications: 1 publications found

Genes affected

LOC105374955 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0344 (5239/152258) while in subpopulation NFE AF = 0.0448 (3046/68018). AF 95% confidence interval is 0.0435. There are 101 homozygotes in GnomAd4. There are 2550 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 101 gene

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: 0.0345 AC: 5242 AN: 152140 Hom.: 101 Cov.: 32

Gnomad AFR AF: 0.0172

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0429

Gnomad ASJ AF: 0.0423

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0342

Gnomad FIN AF: 0.0376

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0448

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0344 AC: 5239 AN: 152258 Hom.: 101 Cov.: 32 AF XY: 0.0343 AC XY: 2550 AN XY: 74442

African (AFR) AF: 0.0171 AC: 712 AN: 41552

American (AMR) AF: 0.0429 AC: 656 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0423 AC: 147 AN: 3472

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5174

South Asian (SAS) AF: 0.0342 AC: 165 AN: 4824

European-Finnish (FIN) AF: 0.0376 AC: 399 AN: 10602

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0448 AC: 3046 AN: 68018

Other (OTH) AF: 0.0402 AC: 85 AN: 2112

Alfa AF: 0.0384 Hom.: 10

Bravo AF: 0.0338

Asia WGS AF: 0.0190 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.5
DANN	Benign	0.82
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs10456831; hg19: chr6-18506764;