12-71938143-G-T

Variant names:

• chr12-71938143-G-T
• rs4570625

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 0.277 in 152,024 control chromosomes in the GnomAD database, including 6,436 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 0.28 (6436 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838
• Publications: 217 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41986 AN: 151906 Hom.: 6424 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.277 AC: 42036 AN: 152024 Hom.: 6436 Cov.: 32 AF XY: 0.277 AC XY: 20562 AN XY: 74304

African (AFR) AF: 0.365 AC: 15128 AN: 41444

American (AMR) AF: 0.283 AC: 4330 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 800 AN: 3470

East Asian (EAS) AF: 0.543 AC: 2803 AN: 5166

South Asian (SAS) AF: 0.286 AC: 1379 AN: 4826

European-Finnish (FIN) AF: 0.190 AC: 2003 AN: 10560

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14728 AN: 67964

Other (OTH) AF: 0.266 AC: 561 AN: 2106

Alfa AF: 0.237 Hom.: 12197

Bravo AF: 0.290

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.18
DANN	Benign	0.17
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs4570625; hg19: chr12-72331923;