chr12-85311097-G-A

Variant names:

• chr12-85311097-G-A
• rs11608773

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 0.242 in 151,888 control chromosomes in the GnomAD database, including 4,781 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 0.24 (4781 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 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: 0.242 AC: 36685 AN: 151770 Hom.: 4780 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.242 AC: 36688 AN: 151888 Hom.: 4781 Cov.: 32 AF XY: 0.240 AC XY: 17780 AN XY: 74226

African (AFR) AF: 0.156 AC: 6477 AN: 41446

American (AMR) AF: 0.252 AC: 3835 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1065 AN: 3466

East Asian (EAS) AF: 0.163 AC: 839 AN: 5154

South Asian (SAS) AF: 0.246 AC: 1184 AN: 4810

European-Finnish (FIN) AF: 0.242 AC: 2558 AN: 10554

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19873 AN: 67910

Other (OTH) AF: 0.235 AC: 494 AN: 2102

Alfa AF: 0.261 Hom.: 672

Bravo AF: 0.235

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.49
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs11608773; hg19: chr12-85704875;