rs12072037

chr1-39954534-C-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;