10-36819770-C-T

Variant names:

• chr10-36819770-C-T
• rs10827731

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 0.227 in 152,124 control chromosomes in the GnomAD database, including 4,999 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 0.23 (4999 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 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: 0.227 AC: 34515 AN: 152006 Hom.: 4998 Cov.: 33

Gnomad AFR AF: 0.0624

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.0723

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.227 AC: 34507 AN: 152124 Hom.: 4999 Cov.: 33 AF XY: 0.227 AC XY: 16858 AN XY: 74348

African (AFR) AF: 0.0622 AC: 2583 AN: 41534

American (AMR) AF: 0.206 AC: 3144 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1135 AN: 3470

East Asian (EAS) AF: 0.0717 AC: 369 AN: 5144

South Asian (SAS) AF: 0.176 AC: 849 AN: 4828

European-Finnish (FIN) AF: 0.376 AC: 3978 AN: 10570

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.317 AC: 21544 AN: 67976

Other (OTH) AF: 0.241 AC: 509 AN: 2112

Alfa AF: 0.264 Hom.: 775

Bravo AF: 0.205

Asia WGS AF: 0.126 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.0
DANN	Benign	0.43
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs10827731; hg19: chr10-37108698;