12-96876545-G-T

Variant names:

• chr12-96876545-G-T
• rs185198

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 0.586 in 152,016 control chromosomes in the GnomAD database, including 26,843 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 0.59 (26843 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.707 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: 0.586 AC: 88963 AN: 151898 Hom.: 26797 Cov.: 32

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.586 AC: 89069 AN: 152016 Hom.: 26843 Cov.: 32 AF XY: 0.580 AC XY: 43071 AN XY: 74262

African (AFR) AF: 0.714 AC: 29593 AN: 41472

American (AMR) AF: 0.567 AC: 8662 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1934 AN: 3468

East Asian (EAS) AF: 0.574 AC: 2961 AN: 5160

South Asian (SAS) AF: 0.638 AC: 3064 AN: 4804

European-Finnish (FIN) AF: 0.399 AC: 4209 AN: 10550

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36744 AN: 67980

Other (OTH) AF: 0.562 AC: 1188 AN: 2114

Alfa AF: 0.542 Hom.: 10625

Bravo AF: 0.603

Asia WGS AF: 0.638 AC: 2219 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	1.4
DANN	Benign	0.23
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs185198; hg19: chr12-97270323;