12-84830362-T-C

Variant names:

• chr12-84830362-T-C
• rs7968335

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 0.593 in 144,212 control chromosomes in the GnomAD database, including 24,731 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 (24731 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 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: 0.593 AC: 85433 AN: 144108 Hom.: 24710 Cov.: 25

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.593 AC: 85503 AN: 144212 Hom.: 24731 Cov.: 25 AF XY: 0.594 AC XY: 41598 AN XY: 70024

African (AFR) AF: 0.539 AC: 20895 AN: 38776

American (AMR) AF: 0.677 AC: 9821 AN: 14504

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2206 AN: 3418

East Asian (EAS) AF: 0.708 AC: 3504 AN: 4952

South Asian (SAS) AF: 0.525 AC: 2368 AN: 4514

European-Finnish (FIN) AF: 0.549 AC: 4996 AN: 9102

Middle Eastern (MID) AF: 0.695 AC: 185 AN: 266

European-Non Finnish (NFE) AF: 0.601 AC: 39539 AN: 65782

Other (OTH) AF: 0.626 AC: 1250 AN: 1998

Alfa AF: 0.563 Hom.: 12168

Bravo AF: 0.584

Asia WGS AF: 0.602 AC: 2053 AN: 3412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.5
DANN	Benign	0.50
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs7968335; hg19: chr12-85224141;