rs17108179

Positions:

• chr10-93106921-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000433227.1(NIP7P1):​n.463T>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.066 in 197,334 control chromosomes in the GnomAD database, including 544 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 0.066 (427 hom., cov: 33)
  • Exomes 𝑓: 0.065 (117 hom.)
• Consequence: NIP7P1 ENST00000433227.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.29

Genes affected

NIP7P1 (HGNC:45180): (NIP7 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NIP7P1	ENST00000433227.1	n.463T>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0664 AC: 10098 AN: 152128 Hom.: 427 Cov.: 33

Gnomad AFR AF: 0.0263

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0514

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0610

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0876

Gnomad OTH AF: 0.0732

GnomAD4 exome AF: 0.0650 AC: 2932 AN: 45088 Hom.: 117 Cov.: 0 AF XY: 0.0674 AC XY: 1708 AN XY: 25334

Gnomad4 AFR exome AF: 0.0171

Gnomad4 AMR exome AF: 0.0293

Gnomad4 ASJ exome AF: 0.121

Gnomad4 EAS exome AF: 0.000373

Gnomad4 SAS exome AF: 0.0382

Gnomad4 FIN exome AF: 0.0975

Gnomad4 NFE exome AF: 0.0729

Gnomad4 OTH exome AF: 0.0615

GnomAD4 genome AF: 0.0663 AC: 10101 AN: 152246 Hom.: 427 Cov.: 33 AF XY: 0.0673 AC XY: 5009 AN XY: 74430

Gnomad4 AFR AF: 0.0262

Gnomad4 AMR AF: 0.0513

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0615

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0876

Gnomad4 OTH AF: 0.0729

Alfa AF: 0.0831 Hom.: 588

Bravo AF: 0.0591

Asia WGS AF: 0.0220 AC: 77 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	10
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17108179; hg19: chr10-94866678;