10-83868459-C-T

Variant names:

• chr10-83868459-C-T
• rs11200713

Variant summary

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

The variant allele was found at a frequency of 0.403 in 151,642 control chromosomes in the GnomAD database, including 12,403 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 (12403 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.429 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: 0.403 AC: 61014 AN: 151522 Hom.: 12379 Cov.: 31

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.403 AC: 61088 AN: 151642 Hom.: 12403 Cov.: 31 AF XY: 0.400 AC XY: 29636 AN XY: 74112

African (AFR) AF: 0.384 AC: 15869 AN: 41294

American (AMR) AF: 0.437 AC: 6673 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1514 AN: 3452

East Asian (EAS) AF: 0.332 AC: 1713 AN: 5162

South Asian (SAS) AF: 0.352 AC: 1689 AN: 4804

European-Finnish (FIN) AF: 0.313 AC: 3304 AN: 10552

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.425 AC: 28806 AN: 67818

Other (OTH) AF: 0.440 AC: 928 AN: 2108

Alfa AF: 0.421 Hom.: 41800

Bravo AF: 0.416

Asia WGS AF: 0.323 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.35
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs11200713; hg19: chr10-85628215;