ENST00000565118.3:n.539_540insC

Variant names:

• chr16-18572974-G-GC
• rs72664299
• ENST00000565118.3:n.539_540insC

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The ENST00000565118.3(ABCC6P1):​n.539_540insC variant causes a non coding transcript exon change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 30)
• Consequence: ABCC6P1 ENST00000565118.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.06
• Publications: 0 publications found

Genes affected

ABCC6P1 (HGNC:):

ABCC6P1 (HGNC:33352): (ATP binding cassette subfamily C member 6 pseudogene 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565118.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCC6P1	NR_003569.1		n.162_163insC		non_coding_transcript_exon	Exon 2 of 10

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCC6P1	ENST00000565118.3	TSL:1	n.539_540insC		non_coding_transcript_exon	Exon 2 of 2
	ABCC6P1	ENST00000546162.6	TSL:2	n.222_223insC		non_coding_transcript_exon	Exon 2 of 11
	ABCC6P1	ENST00000565566.1	TSL:6	n.127_128insC		non_coding_transcript_exon	Exon 2 of 9

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.1

Splicing

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

Other links and lift over

dbSNP: rs72664299; hg19: chr16-18584296;