rs8614

Variant names:

• chr17-29261788-C-A
• rs8614
• NM_020772.3:c.*2751G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-29261788-C-A
• chr17-29261788-C-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_020772.3(NUFIP2):​c.*2751G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,492 control chromosomes in the GnomAD database, including 2,681 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 0.16 (2678 hom., cov: 32)
  • Exomes 𝑓: 0.20 (3 hom.)
• Consequence: NUFIP2 NM_020772.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41
• Publications: 37 publications found

Genes affected

NUFIP2 (HGNC:17634): (nuclear FMR1 interacting protein 2) Enables RNA binding activity. Located in cytoplasmic stress granule; cytosol; and nuclear body. Part of polysomal ribosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020772.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUFIP2	NM_020772.3	MANE Select	c.*2751G>T		3_prime_UTR	Exon 4 of 4	NP_065823.1	Q7Z417-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUFIP2	ENST00000225388.9	TSL:1 MANE Select	c.*2751G>T		3_prime_UTR	Exon 4 of 4	ENSP00000225388.3	Q7Z417-1

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23987 AN: 151940 Hom.: 2676 Cov.: 32

Gnomad AFR AF: 0.0413

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.184

GnomAD4 exome AF: 0.196 AC: 85 AN: 434 Hom.: 3 Cov.: 0 AF XY: 0.183 AC XY: 48 AN XY: 262

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) AF: 0.197 AC: 84 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.158 AC: 23993 AN: 152058 Hom.: 2678 Cov.: 32 AF XY: 0.159 AC XY: 11787 AN XY: 74332

African (AFR) AF: 0.0413 AC: 1714 AN: 41506

American (AMR) AF: 0.205 AC: 3127 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 745 AN: 3466

East Asian (EAS) AF: 0.538 AC: 2783 AN: 5174

South Asian (SAS) AF: 0.248 AC: 1198 AN: 4824

European-Finnish (FIN) AF: 0.142 AC: 1502 AN: 10568

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.181 AC: 12302 AN: 67932

Other (OTH) AF: 0.184 AC: 389 AN: 2112

Alfa AF: 0.179 Hom.: 5002

Bravo AF: 0.161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	14
DANN	Benign	0.81
PhyloP100		1.4
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: rs8614; hg19: chr17-27588806;