NM_005385.4:c.59-5406G>A

Variant names:

• chr3-42612164-G-A
• rs663673
• NM_005385.4:c.59-5406G>A

Variant summary

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

The NM_005385.4(NKTR):​c.59-5406G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,090 control chromosomes in the GnomAD database, including 18,913 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 0.46 (18913 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: NKTR NM_005385.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 3 publications found

Genes affected

NKTR (HGNC:7833): (natural killer cell triggering receptor) This gene encodes a membrane-anchored protein with a hydrophobic amino terminal domain and a cyclophilin-like PPIase domain. It is present on the surface of natural killer cells and facilitates their binding to targets. Its expression is regulated by IL2 activation of the cells. [provided by RefSeq, Jul 2008]

ZBTB47-AS1 (HGNC:41174): (ZBTB47 and NKTR antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKTR	NM_005385.4	c.59-5406G>A		intron_variant	Intron 2 of 16	ENST00000232978.13	NP_005376.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKTR	ENST00000232978.13	c.59-5406G>A		intron_variant	Intron 2 of 16	1	NM_005385.4	ENSP00000232978.8

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70337 AN: 151970 Hom.: 18869 Cov.: 33

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.436

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.463 AC: 70439 AN: 152088 Hom.: 18913 Cov.: 33 AF XY: 0.464 AC XY: 34474 AN XY: 74334

African (AFR) AF: 0.742 AC: 30754 AN: 41460

American (AMR) AF: 0.321 AC: 4911 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1076 AN: 3472

East Asian (EAS) AF: 0.597 AC: 3095 AN: 5184

South Asian (SAS) AF: 0.500 AC: 2409 AN: 4818

European-Finnish (FIN) AF: 0.339 AC: 3578 AN: 10566

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23375 AN: 67986

Other (OTH) AF: 0.437 AC: 922 AN: 2110

Alfa AF: 0.421 Hom.: 5483

Bravo AF: 0.470

Asia WGS AF: 0.525 AC: 1828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.22
PhyloP100		-0.29
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs663673; hg19: chr3-42653656;