chr12-122716961-A-G

Position:

• chr12-122716961-A-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 0.536 in 531,082 control chromosomes in the GnomAD database, including 79,952 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 0.53 (21476 hom., cov: 27)
  • Exomes 𝑓: 0.54 (58476 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.57 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: 0.529 AC: 79455 AN: 150202 Hom.: 21477 Cov.: 27

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.527

GnomAD4 exome AF: 0.539 AC: 205415 AN: 380764 Hom.: 58476 AF XY: 0.531 AC XY: 104606 AN XY: 197082

Gnomad4 AFR exome AF: 0.498

Gnomad4 AMR exome AF: 0.426

Gnomad4 ASJ exome AF: 0.586

Gnomad4 EAS exome AF: 0.560

Gnomad4 SAS exome AF: 0.332

Gnomad4 FIN exome AF: 0.503

Gnomad4 NFE exome AF: 0.573

Gnomad4 OTH exome AF: 0.526

GnomAD4 genome AF: 0.529 AC: 79456 AN: 150318 Hom.: 21476 Cov.: 27 AF XY: 0.520 AC XY: 38020 AN XY: 73140

Gnomad4 AFR AF: 0.503

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.520

Alfa AF: 0.447 Hom.: 1341

Bravo AF: 0.532

Asia WGS AF: 0.383 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	16
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2256572; hg19: chr12-123201508;