6-31275826-C-T

Variant names:

• chr6-31275826-C-T
• rs2524077
• ENST00000494673.1:n.255C>T

Variant summary

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

The ENST00000494673.1(USP8P1):​n.255C>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 0.114 in 819,804 control chromosomes in the GnomAD database, including 6,165 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 0.12 (1135 hom., cov: 32)
  • Exomes 𝑓: 0.11 (5030 hom.)
• Consequence: USP8P1 ENST00000494673.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 15 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USP8P1	ENST00000494673.1	TSL:6	n.255C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000298396	ENST00000755297.1		n.32+4720C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17865 AN: 152048 Hom.: 1134 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0766

Gnomad FIN AF: 0.0514

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.128

GnomAD4 exome AF: 0.113 AC: 75401 AN: 667638 Hom.: 5030 Cov.: 8 AF XY: 0.109 AC XY: 39170 AN XY: 360684

African (AFR) AF: 0.120 AC: 2129 AN: 17688

American (AMR) AF: 0.136 AC: 5821 AN: 42774

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 3391 AN: 20120

East Asian (EAS) AF: 0.0985 AC: 3550 AN: 36030

South Asian (SAS) AF: 0.0485 AC: 3369 AN: 69506

European-Finnish (FIN) AF: 0.0559 AC: 2890 AN: 51736

Middle Eastern (MID) AF: 0.0618 AC: 245 AN: 3966

European-Non Finnish (NFE) AF: 0.127 AC: 49640 AN: 392174

Other (OTH) AF: 0.130 AC: 4366 AN: 33644

GnomAD4 genome AF: 0.117 AC: 17865 AN: 152166 Hom.: 1135 Cov.: 32 AF XY: 0.112 AC XY: 8354 AN XY: 74380

African (AFR) AF: 0.120 AC: 4988 AN: 41500

American (AMR) AF: 0.122 AC: 1873 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 578 AN: 3470

East Asian (EAS) AF: 0.112 AC: 579 AN: 5178

South Asian (SAS) AF: 0.0762 AC: 367 AN: 4816

European-Finnish (FIN) AF: 0.0514 AC: 544 AN: 10584

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8534 AN: 68008

Other (OTH) AF: 0.127 AC: 269 AN: 2112

Alfa AF: 0.123 Hom.: 1885

Bravo AF: 0.125

Asia WGS AF: 0.0950 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.8
DANN	Benign	0.72
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs2524077; hg19: chr6-31243603; COSMIC: COSV66117359; COSMIC: COSV66117359;