rs10506735

Variant names:

• chr12-77214583-G-A
• rs10506735

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.0427

Gnomad4 ASJ AF: 0.0424

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0205

Gnomad4 FIN AF: 0.0191

Gnomad4 NFE AF: 0.0265

Gnomad4 OTH AF: 0.0706

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506735; hg19: chr12-77608363;