rs12072037

Variant names:

• chr1-39954534-C-A
• rs12072037

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 0.0661 in 152,358 control chromosomes in the GnomAD database, including 903 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 0.066 (903 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.419

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 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: 0.0660 AC: 10050 AN: 152240 Hom.: 899 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.0393

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00475

Gnomad OTH AF: 0.0664

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

GnomAD4 genome AF: 0.0661 AC: 10075 AN: 152358 Hom.: 903 Cov.: 32 AF XY: 0.0710 AC XY: 5293 AN XY: 74500

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0118

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.0735

Gnomad4 FIN AF: 0.0393

Gnomad4 NFE AF: 0.00475

Gnomad4 OTH AF: 0.0667

Alfa AF: 0.0225 Hom.: 699

Bravo AF: 0.0761

Asia WGS AF: 0.266 AC: 923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12072037; hg19: chr1-40420206;