NM_025081.3:c.2642+64T>A

Variant names:

• chr14-24411514-T-A
• rs2273635
• NM_025081.3:c.2642+64T>A

Variant summary

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

The NM_025081.3(NYNRIN):​c.2642+64T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0104 in 1,392,164 control chromosomes in the GnomAD database, including 635 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 0.013 (73 hom., cov: 32)
  • Exomes 𝑓: 0.010 (562 hom.)
• Consequence: NYNRIN NM_025081.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02
• Publications: 4 publications found

Genes affected

NYNRIN (HGNC:20165): (NYN domain and retroviral integrase containing) Predicted to enable endoribonuclease activity and mRNA binding activity. Predicted to be involved in RNA phosphodiester bond hydrolysis, endonucleolytic. Predicted to be integral component of membrane. Predicted to be active in cytoplasmic ribonucleoprotein granule and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025081.3. 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
	NYNRIN	NM_025081.3	MANE Select	c.2642+64T>A		intron	N/A	NP_079357.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NYNRIN	ENST00000382554.4	TSL:5 MANE Select	c.2642+64T>A		intron	N/A	ENSP00000371994.3

Frequencies

GnomAD3 genomes AF: 0.0131 AC: 1986 AN: 151974 Hom.: 73 Cov.: 32

Gnomad AFR AF: 0.0144

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0166

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0743

Gnomad FIN AF: 0.00226

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.000898

Gnomad OTH AF: 0.00768

GnomAD4 exome AF: 0.0100 AC: 12450 AN: 1240074 Hom.: 562 AF XY: 0.0115 AC XY: 7223 AN XY: 627494

African (AFR) AF: 0.0133 AC: 384 AN: 28846

American (AMR) AF: 0.0230 AC: 1006 AN: 43680

Ashkenazi Jewish (ASJ) AF: 0.00265 AC: 65 AN: 24498

East Asian (EAS) AF: 0.112 AC: 4347 AN: 38738

South Asian (SAS) AF: 0.0622 AC: 5099 AN: 81928

European-Finnish (FIN) AF: 0.00349 AC: 179 AN: 51262

Middle Eastern (MID) AF: 0.00374 AC: 20 AN: 5350

European-Non Finnish (NFE) AF: 0.000560 AC: 511 AN: 912682

Other (OTH) AF: 0.0158 AC: 839 AN: 53090

GnomAD4 genome AF: 0.0130 AC: 1978 AN: 152090 Hom.: 73 Cov.: 32 AF XY: 0.0150 AC XY: 1112 AN XY: 74338

African (AFR) AF: 0.0144 AC: 597 AN: 41500

American (AMR) AF: 0.0167 AC: 256 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00374 AC: 13 AN: 3472

East Asian (EAS) AF: 0.128 AC: 659 AN: 5156

South Asian (SAS) AF: 0.0733 AC: 352 AN: 4804

European-Finnish (FIN) AF: 0.00226 AC: 24 AN: 10606

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.000898 AC: 61 AN: 67956

Other (OTH) AF: 0.00713 AC: 15 AN: 2104

Alfa AF: 0.00540 Hom.: 4

Bravo AF: 0.0129

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	1.2
DANN	Benign	0.88
PhyloP100		-3.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2273635; hg19: chr14-24880720;