rs12572077

Positions:

• chr10-36818327-C-A
• chr10-36818327-C-G

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 0.393 in 152,092 control chromosomes in the GnomAD database, including 12,362 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 0.39 (12362 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59782 AN: 151974 Hom.: 12352 Cov.: 33

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.393 AC: 59809 AN: 152092 Hom.: 12362 Cov.: 33 AF XY: 0.402 AC XY: 29857 AN XY: 74332

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.390

Alfa AF: 0.390 Hom.: 5574

Bravo AF: 0.391

Asia WGS AF: 0.665 AC: 2309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12572077; hg19: chr10-37107255;