rs10506909

Variant names:

• chr12-84627748-G-A
• rs10506909

Your query was ambiguous. Multiple possible variants found:

• chr12-84627748-G-A
• chr12-84627748-G-T

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 0.0264 in 152,152 control chromosomes in the GnomAD database, including 108 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 0.026 (108 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.104 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: 0.0263 AC: 4005 AN: 152034 Hom.: 107 Cov.: 32

Gnomad AFR AF: 0.0273

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.00721

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0338

Gnomad FIN AF: 0.0353

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00962

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0264 AC: 4010 AN: 152152 Hom.: 108 Cov.: 32 AF XY: 0.0287 AC XY: 2133 AN XY: 74370

African (AFR) AF: 0.0273 AC: 1134 AN: 41514

American (AMR) AF: 0.0641 AC: 979 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.00721 AC: 25 AN: 3468

East Asian (EAS) AF: 0.112 AC: 577 AN: 5150

South Asian (SAS) AF: 0.0341 AC: 164 AN: 4816

European-Finnish (FIN) AF: 0.0353 AC: 374 AN: 10608

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00962 AC: 654 AN: 68010

Other (OTH) AF: 0.0246 AC: 52 AN: 2110

Alfa AF: 0.0156 Hom.: 11

Bravo AF: 0.0301

Asia WGS AF: 0.0920 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.59
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs10506909; hg19: chr12-85021527;