chr10-36818327-C-A

Variant names:

• chr10-36818327-C-A
• rs12572077

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 0.393 in 152,092 control chromosomes in the GnomAD database, including 12,362 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 0.39 (12362 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 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: 0.393 AC: 59782 AN: 151974 Hom.: 12352 Cov.: 33

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.393 AC: 59809 AN: 152092 Hom.: 12362 Cov.: 33 AF XY: 0.402 AC XY: 29857 AN XY: 74332

African (AFR) AF: 0.347 AC: 14402 AN: 41470

American (AMR) AF: 0.445 AC: 6805 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1195 AN: 3472

East Asian (EAS) AF: 0.741 AC: 3823 AN: 5162

South Asian (SAS) AF: 0.628 AC: 3026 AN: 4822

European-Finnish (FIN) AF: 0.397 AC: 4200 AN: 10572

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.369 AC: 25110 AN: 67990

Other (OTH) AF: 0.390 AC: 823 AN: 2110

Alfa AF: 0.387 Hom.: 6149

Bravo AF: 0.391

Asia WGS AF: 0.665 AC: 2309 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	1.5
DANN	Benign	0.49
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs12572077; hg19: chr10-37107255;