rs1512981

Positions:

• chr12-70997303-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 0.572 in 151,822 control chromosomes in the GnomAD database, including 25,481 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 0.57 (25481 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 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: 0.572 AC: 86738 AN: 151704 Hom.: 25443 Cov.: 31

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.572 AC: 86828 AN: 151822 Hom.: 25481 Cov.: 31 AF XY: 0.570 AC XY: 42312 AN XY: 74192

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.550

Alfa AF: 0.544 Hom.: 2882

Bravo AF: 0.582

Asia WGS AF: 0.612 AC: 2130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.56
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: rs1512981; hg19: chr12-71391083;