rs10506065

Variant names:

• chr12-30298107-C-A
• rs10506065

Your query was ambiguous. Multiple possible variants found:

• chr12-30298107-C-A
• chr12-30298107-C-G
• chr12-30298107-C-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 0.308 in 152,074 control chromosomes in the GnomAD database, including 8,317 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 0.31 (8317 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.18
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 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: 0.308 AC: 46832 AN: 151956 Hom.: 8316 Cov.: 33

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.308 AC: 46841 AN: 152074 Hom.: 8317 Cov.: 33 AF XY: 0.313 AC XY: 23286 AN XY: 74316

African (AFR) AF: 0.136 AC: 5637 AN: 41510

American (AMR) AF: 0.439 AC: 6710 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1027 AN: 3470

East Asian (EAS) AF: 0.576 AC: 2973 AN: 5164

South Asian (SAS) AF: 0.458 AC: 2206 AN: 4818

European-Finnish (FIN) AF: 0.321 AC: 3378 AN: 10534

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.350 AC: 23797 AN: 67994

Other (OTH) AF: 0.324 AC: 683 AN: 2106

Alfa AF: 0.321 Hom.: 4153

Bravo AF: 0.308

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.19
PhyloP100		-4.2

Splicing

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

Other links and lift over

dbSNP: rs10506065; hg19: chr12-30451040;