12-84849902-A-G

Variant names:

• chr12-84849902-A-G
• rs6539870

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 0.341 in 151,922 control chromosomes in the GnomAD database, including 10,231 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 0.34 (10231 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 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: 0.341 AC: 51790 AN: 151804 Hom.: 10219 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.00637

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.341 AC: 51843 AN: 151922 Hom.: 10231 Cov.: 32 AF XY: 0.327 AC XY: 24247 AN XY: 74250

African (AFR) AF: 0.518 AC: 21439 AN: 41420

American (AMR) AF: 0.286 AC: 4361 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1337 AN: 3466

East Asian (EAS) AF: 0.00638 AC: 33 AN: 5170

South Asian (SAS) AF: 0.138 AC: 667 AN: 4820

European-Finnish (FIN) AF: 0.166 AC: 1763 AN: 10596

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21075 AN: 67900

Other (OTH) AF: 0.354 AC: 745 AN: 2106

Alfa AF: 0.319 Hom.: 13715

Bravo AF: 0.364

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.53
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs6539870; hg19: chr12-85243681;