3-139495061-A-G

Position:

• chr3-139495061-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 0.46 in 532,106 control chromosomes in the GnomAD database, including 64,399 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 (24209 hom., cov: 33)
  • Exomes 𝑓: 0.43 (40190 hom.)
• Consequence: ACTG1P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

Genes affected

ACTG1P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACTG1P1		n.139495061A>G		intragenic_variant
COPB2-DT	NR_121609.1	n.354+71947A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COPB2-DT	ENST00000515247.5	n.317+71947A>G		intron_variant		4
COPB2-DT	ENST00000655667.1	n.595+71947A>G		intron_variant
COPB2-DT	ENST00000658348.1	n.671+71947A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80695 AN: 152052 Hom.: 24154 Cov.: 33

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.487

GnomAD4 exome AF: 0.431 AC: 163924 AN: 379938 Hom.: 40190 AF XY: 0.428 AC XY: 87175 AN XY: 203544

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 0.655

Gnomad4 ASJ exome AF: 0.398

Gnomad4 EAS exome AF: 0.921

Gnomad4 SAS exome AF: 0.434

Gnomad4 FIN exome AF: 0.307

Gnomad4 NFE exome AF: 0.368

Gnomad4 OTH exome AF: 0.446

GnomAD4 genome AF: 0.531 AC: 80808 AN: 152168 Hom.: 24209 Cov.: 33 AF XY: 0.532 AC XY: 39567 AN XY: 74388

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.488

Alfa AF: 0.409 Hom.: 2298

Bravo AF: 0.570

Asia WGS AF: 0.686 AC: 2384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.2
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs295470; hg19: chr3-139213903;