12-71938143-G-T

Position:

• chr12-71938143-G-T

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 0.277 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.266

Alfa AF: 0.215 Hom.: 3735

Bravo AF: 0.290

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4570625; hg19: chr12-72331923;