rs11008020

Positions:

• chr10-30380788-A-T

Variant summary

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

The ENST00000398317.2(NIFKP1):​n.615A>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 0.29 in 597,298 control chromosomes in the GnomAD database, including 28,535 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 0.24 (5527 hom., cov: 32)
  • Exomes 𝑓: 0.31 (23008 hom.)
• Consequence: NIFKP1 ENST00000398317.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

Genes affected

NIFKP1 (HGNC:44949): (NIFK pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NIFKP1	ENST00000398317.2	n.615A>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36794 AN: 152108 Hom.: 5528 Cov.: 32

Gnomad AFR AF: 0.0698

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.0488

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.272

GnomAD4 exome AF: 0.307 AC: 136618 AN: 445072 Hom.: 23008 Cov.: 3 AF XY: 0.308 AC XY: 73771 AN XY: 239796

Gnomad4 AFR exome AF: 0.0721

Gnomad4 AMR exome AF: 0.268

Gnomad4 ASJ exome AF: 0.290

Gnomad4 EAS exome AF: 0.0482

Gnomad4 SAS exome AF: 0.286

Gnomad4 FIN exome AF: 0.374

Gnomad4 NFE exome AF: 0.346

Gnomad4 OTH exome AF: 0.297

GnomAD4 genome AF: 0.242 AC: 36797 AN: 152226 Hom.: 5527 Cov.: 32 AF XY: 0.240 AC XY: 17895 AN XY: 74434

Gnomad4 AFR AF: 0.0696

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.0487

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.269

Alfa AF: 0.285 Hom.: 843

Bravo AF: 0.227

Asia WGS AF: 0.141 AC: 493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11008020; hg19: chr10-30669717;