5-142152170-C-T

Variant names:

• chr5-142152170-C-T
• rs249637
• NM_030571.4:c.*442C>T

Variant summary

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

The NM_030571.4(NDFIP1):​c.*442C>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 0.937 in 152,850 control chromosomes in the GnomAD database, including 67,127 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 0.94 (66877 hom., cov: 32)
  • Exomes 𝑓: 0.94 (250 hom.)
• Consequence: NDFIP1 NM_030571.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58
• Publications: 7 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

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.*442C>T		3_prime_UTR	Exon 8 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.*442C>T		3_prime_UTR	Exon 8 of 8	ENSP00000253814.3	Q9BT67-1
	NDFIP1	ENST00000944183.1		c.*442C>T		3_prime_UTR	Exon 9 of 9	ENSP00000614242.1
	NDFIP1	ENST00000856977.1		c.*442C>T		3_prime_UTR	Exon 8 of 8	ENSP00000527036.1

Frequencies

GnomAD3 genomes AF: 0.937 AC: 142527 AN: 152162 Hom.: 66819 Cov.: 32

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.981

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.937

GnomAD4 exome AF: 0.939 AC: 535 AN: 570 Hom.: 250 Cov.: 0 AF XY: 0.932 AC XY: 313 AN XY: 336

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.913 AC: 126 AN: 138

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.946 AC: 403 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 1.00 AC: 4 AN: 4

GnomAD4 genome AF: 0.937 AC: 142645 AN: 152280 Hom.: 66877 Cov.: 32 AF XY: 0.940 AC XY: 69957 AN XY: 74458

African (AFR) AF: 0.947 AC: 39329 AN: 41552

American (AMR) AF: 0.945 AC: 14444 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3039 AN: 3466

East Asian (EAS) AF: 0.999 AC: 5183 AN: 5188

South Asian (SAS) AF: 0.981 AC: 4739 AN: 4830

European-Finnish (FIN) AF: 0.951 AC: 10089 AN: 10608

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.922 AC: 62713 AN: 68024

Other (OTH) AF: 0.938 AC: 1982 AN: 2114

Alfa AF: 0.926 Hom.: 82468

Bravo AF: 0.935

Asia WGS AF: 0.988 AC: 3434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	14
DANN	Benign	0.48
PhyloP100		1.6
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: rs249637; hg19: chr5-141531735;