12-84526555-T-C

Variant names:

• chr12-84526555-T-C
• rs1031681

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.544 in 151,658 control chromosomes in the GnomAD database, including 23,120 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 0.54 (23120 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.744 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: 0.544 AC: 82497 AN: 151540 Hom.: 23113 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.544 AC: 82551 AN: 151658 Hom.: 23120 Cov.: 31 AF XY: 0.547 AC XY: 40537 AN XY: 74092

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.518

Alfa AF: 0.525 Hom.: 4218

Bravo AF: 0.527

Asia WGS AF: 0.581 AC: 2019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.13
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1031681; hg19: chr12-84920334;