rs61003310

chr12-56116165-GA-Gchr12-56116165-GA-GAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.0786 in 231,732 control chromosomes in the GnomAD database, including 1,069 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.14 (828 hom., cov: 17)
  • Exomes 𝑓: 0.039 (241 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 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: 0.143 AC: 12681 AN: 88420 Hom.: 827 Cov.: 17

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0913

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0979

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.108

GnomAD3 exomes AF: 0.00371 AC: 210 AN: 56562 Hom.: 6 AF XY: 0.00365 AC XY: 118 AN XY: 32310

Gnomad AFR exome AF: 0.0249

Gnomad AMR exome AF: 0.00458

Gnomad ASJ exome AF: 0.00365

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00278

Gnomad FIN exome AF: 0.00282

Gnomad NFE exome AF: 0.00298

Gnomad OTH exome AF: 0.00426

GnomAD4 exome AF: 0.0385 AC: 5517 AN: 143224 Hom.: 241 Cov.: 0 AF XY: 0.0360 AC XY: 3078 AN XY: 85412

Gnomad4 AFR exome AF: 0.143

Gnomad4 AMR exome AF: 0.0272

Gnomad4 ASJ exome AF: 0.0217

Gnomad4 EAS exome AF: 0.00130

Gnomad4 SAS exome AF: 0.0414

Gnomad4 FIN exome AF: 0.0461

Gnomad4 NFE exome AF: 0.0377

Gnomad4 OTH exome AF: 0.0407

GnomAD4 genome AF: 0.143 AC: 12691 AN: 88508 Hom.: 828 Cov.: 17 AF XY: 0.144 AC XY: 6023 AN XY: 41862

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.0910

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0841

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.107

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61003310; hg19: chr12-56509949;