chr6-117630952-C-T

Variant names:

• chr6-117630952-C-T
• rs9285426

Variant summary

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

The variant allele was found at a frequency of 0.426 in 152,006 control chromosomes in the GnomAD database, including 15,240 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 0.43 (15240 hom., cov: 32)
• Consequence: NEPNP intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 4 publications found

Genes affected

NEPNP (HGNC:33184): (nephrocan, pseudogene) Nephrocan is a secreted glycoprotein that acts as an inhibitor of the transforming growth factor-beta signaling pathway. This gene has been inactivated by mutation and is nonfunctional in humans. [provided by RefSeq, May 2010]

ENSG00000289372 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815930.1. 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
	ENSG00000289372	ENST00000815930.1		n.629-21806G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64824 AN: 151888 Hom.: 15244 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.426 AC: 64827 AN: 152006 Hom.: 15240 Cov.: 32 AF XY: 0.436 AC XY: 32358 AN XY: 74298

African (AFR) AF: 0.254 AC: 10522 AN: 41444

American (AMR) AF: 0.409 AC: 6248 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1402 AN: 3466

East Asian (EAS) AF: 0.220 AC: 1137 AN: 5164

South Asian (SAS) AF: 0.625 AC: 3015 AN: 4822

European-Finnish (FIN) AF: 0.653 AC: 6904 AN: 10568

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.500 AC: 33964 AN: 67962

Other (OTH) AF: 0.433 AC: 913 AN: 2108

Alfa AF: 0.455 Hom.: 6421

Bravo AF: 0.394

Asia WGS AF: 0.415 AC: 1444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.55
DANN	Benign	0.61
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9285426; hg19: chr6-117952115;