chr12-84447185-A-G

Variant names:

• chr12-84447185-A-G
• rs11116408

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 0.402 in 151,706 control chromosomes in the GnomAD database, including 12,593 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 0.40 (12593 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 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: 0.402 AC: 60887 AN: 151588 Hom.: 12588 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.402 AC: 60925 AN: 151706 Hom.: 12593 Cov.: 32 AF XY: 0.400 AC XY: 29614 AN XY: 74096

African (AFR) AF: 0.383 AC: 15853 AN: 41396

American (AMR) AF: 0.474 AC: 7208 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1909 AN: 3464

East Asian (EAS) AF: 0.198 AC: 1015 AN: 5126

South Asian (SAS) AF: 0.538 AC: 2591 AN: 4814

European-Finnish (FIN) AF: 0.308 AC: 3248 AN: 10544

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27611 AN: 67836

Other (OTH) AF: 0.443 AC: 932 AN: 2104

Alfa AF: 0.413 Hom.: 6841

Bravo AF: 0.412

Asia WGS AF: 0.375 AC: 1307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.7
DANN	Benign	0.20
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs11116408; hg19: chr12-84840964;