ENST00000731087.1:n.2095A>T

Variant names:

• chr3-139495628-A-T
• rs2165139
• ENST00000731087.1:n.2095A>T

Variant summary

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

The ENST00000731087.1(COPB2-DT):​n.2095A>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.151 in 151,590 control chromosomes in the GnomAD database, including 3,823 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 0.15 (3823 hom., cov: 31)
• Consequence: COPB2-DT ENST00000731087.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.73
• 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=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACTG1P1		n.139495628A>T		intragenic_variant
COPB2-DT	NR_121609.1	n.354+72514A>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COPB2-DT	ENST00000731087.1	n.2095A>T		non_coding_transcript_exon_variant	Exon 5 of 5
COPB2-DT	ENST00000731088.1	n.2296A>T		non_coding_transcript_exon_variant	Exon 5 of 5
COPB2-DT	ENST00000731089.1	n.2141A>T		non_coding_transcript_exon_variant	Exon 6 of 6

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22864 AN: 151476 Hom.: 3816 Cov.: 31

Gnomad AFR AF: 0.0453

Gnomad AMI AF: 0.0859

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.0897

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.141

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.151 AC: 22880 AN: 151590 Hom.: 3823 Cov.: 31 AF XY: 0.164 AC XY: 12166 AN XY: 74082

African (AFR) AF: 0.0453 AC: 1877 AN: 41446

American (AMR) AF: 0.339 AC: 5158 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0897 AC: 311 AN: 3468

East Asian (EAS) AF: 0.857 AC: 4423 AN: 5160

South Asian (SAS) AF: 0.275 AC: 1317 AN: 4784

European-Finnish (FIN) AF: 0.189 AC: 1953 AN: 10340

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7445 AN: 67852

Other (OTH) AF: 0.142 AC: 299 AN: 2104

Alfa AF: 0.123 Hom.: 237

Bravo AF: 0.165

Asia WGS AF: 0.499 AC: 1731 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	9.6
DANN	Benign	0.74
PhyloP100		3.7

Splicing

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

Other links and lift over

dbSNP: rs2165139; hg19: chr3-139214470;