chr12-77214583-G-A

Variant names:

• chr12-77214583-G-A
• rs10506735

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 0.0757 in 152,148 control chromosomes in the GnomAD database, including 891 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 0.076 (891 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0756 AC: 11501 AN: 152030 Hom.: 890 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0427

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0205

Gnomad FIN AF: 0.0191

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0265

Gnomad OTH AF: 0.0723

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

GnomAD4 genome AF: 0.0757 AC: 11522 AN: 152148 Hom.: 891 Cov.: 32 AF XY: 0.0736 AC XY: 5474 AN XY: 74394

African (AFR) AF: 0.203 AC: 8439 AN: 41492

American (AMR) AF: 0.0427 AC: 652 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0424 AC: 147 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5174

South Asian (SAS) AF: 0.0205 AC: 99 AN: 4822

European-Finnish (FIN) AF: 0.0191 AC: 202 AN: 10588

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.0265 AC: 1801 AN: 68010

Other (OTH) AF: 0.0706 AC: 149 AN: 2110

Alfa AF: 0.0461 Hom.: 83

Bravo AF: 0.0841

Asia WGS AF: 0.0230 AC: 79 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.45
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs10506735; hg19: chr12-77608363;