10-36816845-G-C

Variant names:

• chr10-36816845-G-C
• rs2488748

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 0.054 in 152,256 control chromosomes in the GnomAD database, including 269 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 0.054 (269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0726 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: 0.0539 AC: 8202 AN: 152138 Hom.: 267 Cov.: 32

Gnomad AFR AF: 0.0199

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0398

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.0433

Gnomad SAS AF: 0.0669

Gnomad FIN AF: 0.0707

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0743

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0540 AC: 8216 AN: 152256 Hom.: 269 Cov.: 32 AF XY: 0.0535 AC XY: 3985 AN XY: 74442

African (AFR) AF: 0.0200 AC: 830 AN: 41554

American (AMR) AF: 0.0402 AC: 614 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0700 AC: 243 AN: 3472

East Asian (EAS) AF: 0.0436 AC: 225 AN: 5164

South Asian (SAS) AF: 0.0671 AC: 324 AN: 4826

European-Finnish (FIN) AF: 0.0707 AC: 750 AN: 10608

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0743 AC: 5052 AN: 68024

Other (OTH) AF: 0.0511 AC: 108 AN: 2112

Alfa AF: 0.0268 Hom.: 14

Bravo AF: 0.0503

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.71
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs2488748; hg19: chr10-37105773;