3-139495061-A-G

Variant names:

• chr3-139495061-A-G
• rs295470
• ENST00000731087.1:n.1682A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000731087.1(COPB2-DT):​n.1682A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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: COPB2-DT ENST00000731087.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 4 publications found

Genes affected

COPB2-DT (HGNC:55579): (COPB2 divergent transcript)

ACTG1P1 (HGNC:146): (actin gamma 1 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ACTG1P1		n.139495061A>G		intragenic_variant
COPB2-DT	NR_121609.1	n.354+71947A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COPB2-DT	ENST00000731087.1	n.1682A>G		non_coding_transcript_exon_variant	Exon 4 of 5
COPB2-DT	ENST00000731088.1	n.1729A>G		non_coding_transcript_exon_variant	Exon 5 of 5
COPB2-DT	ENST00000731089.1	n.1728A>G		non_coding_transcript_exon_variant	Exon 5 of 6

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

African (AFR) AF: 0.750 AC: 7685 AN: 10244

American (AMR) AF: 0.655 AC: 11151 AN: 17026

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 4262 AN: 10696

East Asian (EAS) AF: 0.921 AC: 20121 AN: 21844

South Asian (SAS) AF: 0.434 AC: 19013 AN: 43788

European-Finnish (FIN) AF: 0.307 AC: 8310 AN: 27064

Middle Eastern (MID) AF: 0.390 AC: 613 AN: 1570

European-Non Finnish (NFE) AF: 0.368 AC: 83347 AN: 226590

Other (OTH) AF: 0.446 AC: 9422 AN: 21116

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

African (AFR) AF: 0.768 AC: 31901 AN: 41518

American (AMR) AF: 0.615 AC: 9408 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1433 AN: 3470

East Asian (EAS) AF: 0.920 AC: 4769 AN: 5182

South Asian (SAS) AF: 0.476 AC: 2296 AN: 4820

European-Finnish (FIN) AF: 0.324 AC: 3425 AN: 10566

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.386 AC: 26232 AN: 68008

Other (OTH) AF: 0.488 AC: 1031 AN: 2114

Alfa AF: 0.422 Hom.: 2534

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
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs295470; hg19: chr3-139213903;