6-31276743-G-T

Variant names:

• chr6-31276743-G-T
• rs2524070
• ENST00000494673.1:n.1172G>T

Variant summary

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

The ENST00000494673.1(USP8P1):​n.1172G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: USP8P1 ENST00000494673.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.60
• Publications: 0 publications found

Genes affected

USP8P1 (HGNC:13987): (USP8 pseudogene 1)

ENSG00000298396 (HGNC:):

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=-0.64).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000494673.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP8P1	ENST00000494673.1	TSL:6	n.1172G>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000298396	ENST00000755297.1		n.32+5637G>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1005320 Hom.: 0 Cov.: 14 AF XY: 0.00 AC XY: 0 AN XY: 500430

African (AFR) AF: 0.00 AC: 0 AN: 20760

American (AMR) AF: 0.00 AC: 0 AN: 21418

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16004

East Asian (EAS) AF: 0.00 AC: 0 AN: 31634

South Asian (SAS) AF: 0.00 AC: 0 AN: 47580

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 42612

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3732

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 779456

Other (OTH) AF: 0.00 AC: 0 AN: 42124

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	11
DANN	Benign	0.63
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs2524070; hg19: chr6-31244520;