rs10506697

Variant names:

• chr12-74561694-A-G
• rs10506697

Your query was ambiguous. Multiple possible variants found:

• chr12-74561694-A-G
• chr12-74561694-A-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 0.0749 in 152,264 control chromosomes in the GnomAD database, including 981 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 0.075 (981 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 2 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 = 0.461 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: 0.0750 AC: 11411 AN: 152146 Hom.: 978 Cov.: 32

Gnomad AFR AF: 0.0754

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0429

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0515

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0370

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0749 AC: 11409 AN: 152264 Hom.: 981 Cov.: 32 AF XY: 0.0791 AC XY: 5889 AN XY: 74454

African (AFR) AF: 0.0752 AC: 3125 AN: 41552

American (AMR) AF: 0.116 AC: 1775 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0429 AC: 149 AN: 3472

East Asian (EAS) AF: 0.477 AC: 2463 AN: 5168

South Asian (SAS) AF: 0.136 AC: 657 AN: 4822

European-Finnish (FIN) AF: 0.0515 AC: 546 AN: 10610

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0370 AC: 2519 AN: 68030

Other (OTH) AF: 0.0719 AC: 152 AN: 2114

Alfa AF: 0.0679 Hom.: 98

Bravo AF: 0.0817

Asia WGS AF: 0.307 AC: 1067 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	6.4
DANN	Benign	0.73
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10506697; hg19: chr12-74955474;