12-65978100-G-T

Variant names:

• chr12-65978100-G-T
• rs7968682

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 0.568 in 151,914 control chromosomes in the GnomAD database, including 25,140 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 0.57 (25140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57
• Publications: 40 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86242 AN: 151796 Hom.: 25110 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.568 AC: 86312 AN: 151914 Hom.: 25140 Cov.: 32 AF XY: 0.575 AC XY: 42675 AN XY: 74252

African (AFR) AF: 0.583 AC: 24159 AN: 41422

American (AMR) AF: 0.626 AC: 9556 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2343 AN: 3470

East Asian (EAS) AF: 0.900 AC: 4662 AN: 5180

South Asian (SAS) AF: 0.753 AC: 3620 AN: 4808

European-Finnish (FIN) AF: 0.503 AC: 5295 AN: 10518

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34762 AN: 67944

Other (OTH) AF: 0.592 AC: 1251 AN: 2114

Alfa AF: 0.537 Hom.: 62392

Bravo AF: 0.582

Asia WGS AF: 0.769 AC: 2667 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	14
DANN	Benign	0.39
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs7968682; hg19: chr12-66371880;