rs6863411

Variant names:

• chr5-142133639-A-T
• rs6863411
• NM_030571.4:c.282+1297A>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.282+1297A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 152,092 control chromosomes in the GnomAD database, including 34,675 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 0.67 (34675 hom., cov: 32)
• Consequence: NDFIP1 NM_030571.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 55 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 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.282+1297A>T		intron	N/A	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.282+1297A>T		intron	N/A	ENSP00000253814.3	Q9BT67-1
	NDFIP1	ENST00000856982.1		c.357+1297A>T		intron	N/A	ENSP00000527041.1
	NDFIP1	ENST00000944183.1		c.282+1297A>T		intron	N/A	ENSP00000614242.1

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102147 AN: 151974 Hom.: 34636 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.678

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.672 AC: 102232 AN: 152092 Hom.: 34675 Cov.: 32 AF XY: 0.671 AC XY: 49894 AN XY: 74340

African (AFR) AF: 0.767 AC: 31835 AN: 41482

American (AMR) AF: 0.680 AC: 10388 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2439 AN: 3470

East Asian (EAS) AF: 0.645 AC: 3336 AN: 5170

South Asian (SAS) AF: 0.562 AC: 2708 AN: 4822

European-Finnish (FIN) AF: 0.662 AC: 6990 AN: 10566

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42323 AN: 67986

Other (OTH) AF: 0.675 AC: 1428 AN: 2114

Alfa AF: 0.650 Hom.: 3999

Bravo AF: 0.681

Asia WGS AF: 0.609 AC: 2121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.6
DANN	Benign	0.75
PhyloP100		-0.28
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: rs6863411; hg19: chr5-141513204;