rs1512981

Variant names:

• chr12-70997303-G-A
• rs1512981

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.693 AC: 28655 AN: 41372

American (AMR) AF: 0.586 AC: 8931 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1646 AN: 3468

East Asian (EAS) AF: 0.503 AC: 2591 AN: 5156

South Asian (SAS) AF: 0.666 AC: 3208 AN: 4818

European-Finnish (FIN) AF: 0.482 AC: 5086 AN: 10544

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34955 AN: 67912

Other (OTH) AF: 0.550 AC: 1159 AN: 2108

Alfa AF: 0.551 Hom.: 3068

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
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1512981; hg19: chr12-71391083;