12-83816983-A-T

Variant names:

• chr12-83816983-A-T
• rs1380756

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 0.689 in 151,630 control chromosomes in the GnomAD database, including 37,612 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 0.69 (37612 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.885 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: 0.689 AC: 104371 AN: 151512 Hom.: 37556 Cov.: 30

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.689 AC: 104487 AN: 151630 Hom.: 37612 Cov.: 30 AF XY: 0.690 AC XY: 51083 AN XY: 74074

African (AFR) AF: 0.892 AC: 36923 AN: 41374

American (AMR) AF: 0.711 AC: 10819 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2363 AN: 3466

East Asian (EAS) AF: 0.753 AC: 3873 AN: 5144

South Asian (SAS) AF: 0.801 AC: 3840 AN: 4796

European-Finnish (FIN) AF: 0.524 AC: 5493 AN: 10476

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38887 AN: 67856

Other (OTH) AF: 0.714 AC: 1502 AN: 2104

Alfa AF: 0.316 Hom.: 453

Bravo AF: 0.713

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.8
DANN	Benign	0.73
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs1380756; hg19: chr12-84210762;