chr10-93106921-A-C

Variant names:

• chr10-93106921-A-C
• rs17108179
• ENST00000433227.1:n.463T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

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 (NFE) allele frequency at 95% confidence interval = 0.0857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NIP7P1		n.93106921A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NIP7P1	ENST00000433227.1	n.463T>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AF: 0.0171 AC: 19 AN: 1108

American (AMR) AF: 0.0293 AC: 138 AN: 4706

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 57 AN: 472

East Asian (EAS) AF: 0.000373 AC: 1 AN: 2682

South Asian (SAS) AF: 0.0382 AC: 160 AN: 4186

European-Finnish (FIN) AF: 0.0975 AC: 1009 AN: 10344

Middle Eastern (MID) AF: 0.0659 AC: 72 AN: 1092

European-Non Finnish (NFE) AF: 0.0729 AC: 1373 AN: 18824

Other (OTH) AF: 0.0615 AC: 103 AN: 1674

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

African (AFR) AF: 0.0262 AC: 1090 AN: 41552

American (AMR) AF: 0.0513 AC: 785 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 524 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0615 AC: 296 AN: 4812

European-Finnish (FIN) AF: 0.117 AC: 1240 AN: 10596

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0876 AC: 5955 AN: 68008

Other (OTH) AF: 0.0729 AC: 154 AN: 2112

Alfa AF: 0.0803 Hom.: 739

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
PhyloP100		4.3

Splicing

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

Other links and lift over

dbSNP: rs17108179; hg19: chr10-94866678;