12-71938143-G-T

Variant names:

• chr12-71938143-G-T
• rs4570625

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;