6-31277284-G-T

Variant names:

• chr6-31277284-G-T
• rs2524068
• ENST00000494673.1:n.1713G>T

Variant summary

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

The ENST00000494673.1(USP8P1):​n.1713G>T 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 0.155 in 794,154 control chromosomes in the GnomAD database, including 10,284 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 0.17 (2256 hom., cov: 32)
  • Exomes 𝑓: 0.15 (8028 hom.)
• Consequence: USP8P1 ENST00000494673.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.866
• Publications: 14 publications found

Genes affected

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

ENSG00000298396 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

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.1713G>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000298396	ENST00000755297.1		n.32+6178G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25774 AN: 152056 Hom.: 2252 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.175

GnomAD4 exome AF: 0.152 AC: 97364 AN: 641978 Hom.: 8028 Cov.: 6 AF XY: 0.146 AC XY: 51047 AN XY: 348452

African (AFR) AF: 0.193 AC: 3424 AN: 17726

American (AMR) AF: 0.162 AC: 7007 AN: 43138

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 3626 AN: 20640

East Asian (EAS) AF: 0.104 AC: 3705 AN: 35672

South Asian (SAS) AF: 0.0676 AC: 4732 AN: 70036

European-Finnish (FIN) AF: 0.114 AC: 5865 AN: 51542

Middle Eastern (MID) AF: 0.0791 AC: 324 AN: 4098

European-Non Finnish (NFE) AF: 0.172 AC: 63009 AN: 366248

Other (OTH) AF: 0.173 AC: 5672 AN: 32878

GnomAD4 genome AF: 0.170 AC: 25795 AN: 152176 Hom.: 2256 Cov.: 32 AF XY: 0.164 AC XY: 12219 AN XY: 74398

African (AFR) AF: 0.198 AC: 8209 AN: 41492

American (AMR) AF: 0.155 AC: 2376 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 623 AN: 3472

East Asian (EAS) AF: 0.121 AC: 626 AN: 5180

South Asian (SAS) AF: 0.100 AC: 483 AN: 4828

European-Finnish (FIN) AF: 0.108 AC: 1149 AN: 10598

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11795 AN: 67998

Other (OTH) AF: 0.176 AC: 371 AN: 2108

Alfa AF: 0.171 Hom.: 5248

Bravo AF: 0.177

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	7.5
DANN	Benign	0.77
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs2524068; hg19: chr6-31245061;