rs2165139

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-139495628-A-G
• chr3-139495628-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000731087.1(COPB2-DT):​n.2095A>G variant causes a non coding transcript exon change. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACTG1P1		n.139495628A>G		intragenic_variant
COPB2-DT	NR_121609.1	n.354+72514A>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.2095A>G		non_coding_transcript_exon_variant	Exon 5 of 5
COPB2-DT	ENST00000731088.1	n.2296A>G		non_coding_transcript_exon_variant	Exon 5 of 5
COPB2-DT	ENST00000731089.1	n.2141A>G		non_coding_transcript_exon_variant	Exon 6 of 6

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	9.9
DANN	Benign	0.71
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;