rs3021529

Positions:

• chr12-63151900-G-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 0.126 in 152,132 control chromosomes in the GnomAD database, including 1,301 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 0.13 (1301 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

Genes affected

(HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.63151900G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000279444	ENST00000624438.1	n.29-581G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19215 AN: 152014 Hom.: 1299 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0380

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0944

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.126 AC: 19235 AN: 152132 Hom.: 1301 Cov.: 32 AF XY: 0.125 AC XY: 9274 AN XY: 74362

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.0383

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.0944

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.121

Alfa AF: 0.140 Hom.: 2008

Bravo AF: 0.123

Asia WGS AF: 0.0980 AC: 338 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	9.1
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3021529; hg19: chr12-63545680;