5-142108799-G-A

Variant names:

• chr5-142108799-G-A
• rs3761759
• NM_030571.4:c.-176G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_030571.4(NDFIP1):​c.-176G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000683 in 292,948 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000068 (0 hom.)
• Consequence: NDFIP1 NM_030571.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 8 publications found

Genes affected

NDFIP1 (HGNC:17592): (Nedd4 family interacting protein 1) The protein encoded by this gene belongs to a small group of evolutionarily conserved proteins with three transmembrane domains. It is a potential target for ubiquitination by the Nedd4 family of proteins. This protein is thought to be part of a family of integral Golgi membrane proteins. [provided by RefSeq, Jul 2008]

ENSG00000300089 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030571.4. 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
	NDFIP1	NM_030571.4	MANE Select	c.-176G>A		5_prime_UTR	Exon 1 of 8	NP_085048.1	Q9BT67-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NDFIP1	ENST00000253814.6	TSL:1 MANE Select	c.-176G>A		5_prime_UTR	Exon 1 of 8	ENSP00000253814.3	Q9BT67-1
	NDFIP1	ENST00000856982.1		c.-176G>A		5_prime_UTR	Exon 1 of 9	ENSP00000527041.1
	NDFIP1	ENST00000856983.1		c.-176G>A		5_prime_UTR	Exon 1 of 7	ENSP00000527042.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000683 AC: 2 AN: 292948 Hom.: 0 Cov.: 5 AF XY: 0.00000663 AC XY: 1 AN XY: 150880

African (AFR) AF: 0.00 AC: 0 AN: 6696

American (AMR) AF: 0.00 AC: 0 AN: 6522

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8680

East Asian (EAS) AF: 0.00 AC: 0 AN: 20554

South Asian (SAS) AF: 0.00 AC: 0 AN: 12078

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21728

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1256

European-Non Finnish (NFE) AF: 0.0000101 AC: 2 AN: 198644

Other (OTH) AF: 0.00 AC: 0 AN: 16790

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 530

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	15
DANN	Benign	0.93
PhyloP100		-0.24
PromoterAI		-0.033	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.0

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: rs3761759; hg19: chr5-141488364;