ENST00000398317.2:n.615A>T

Variant names:

• chr10-30380788-A-T
• rs11008020
• ENST00000398317.2:n.615A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000398317.2. 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
	NIFKP1	ENST00000398317.2	TSL:6	n.615A>T		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.0721 AC: 899 AN: 12466

American (AMR) AF: 0.268 AC: 4898 AN: 18310

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 4076 AN: 14072

East Asian (EAS) AF: 0.0482 AC: 1373 AN: 28508

South Asian (SAS) AF: 0.286 AC: 13807 AN: 48214

European-Finnish (FIN) AF: 0.374 AC: 13073 AN: 34938

Middle Eastern (MID) AF: 0.315 AC: 585 AN: 1856

European-Non Finnish (NFE) AF: 0.346 AC: 90604 AN: 262110

Other (OTH) AF: 0.297 AC: 7303 AN: 24598

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

African (AFR) AF: 0.0696 AC: 2891 AN: 41546

American (AMR) AF: 0.252 AC: 3855 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 935 AN: 3472

East Asian (EAS) AF: 0.0487 AC: 253 AN: 5192

South Asian (SAS) AF: 0.279 AC: 1345 AN: 4828

European-Finnish (FIN) AF: 0.346 AC: 3661 AN: 10582

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22917 AN: 68000

Other (OTH) AF: 0.269 AC: 570 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.63
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs11008020; hg19: chr10-30669717;