NM_018982.5:c.-68C>T

Variant names:

• chr1-53889262-G-A
• rs3817871
• NM_018982.5:c.-68C>T

Variant summary

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

The NM_018982.5(YIPF1):​c.-68C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: YIPF1 NM_018982.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 6 publications found

Genes affected

YIPF1 (HGNC:25231): (Yip1 domain family member 1) Predicted to enable small GTPase binding activity. Predicted to be involved in vesicle-mediated transport. Located in several cellular components, including Golgi apparatus subcompartment; nucleoplasm; and transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018982.5. 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
	YIPF1	NM_018982.5	MANE Select	c.-68C>T		5_prime_UTR	Exon 2 of 11	NP_061855.1
	YIPF1	NR_036639.2		n.287C>T		non_coding_transcript_exon	Exon 2 of 12
	YIPF1	NR_036640.2		n.86-276C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YIPF1	ENST00000072644.7	TSL:1 MANE Select	c.-68C>T		5_prime_UTR	Exon 2 of 11	ENSP00000072644.1
	YIPF1	ENST00000464950.6	TSL:1	n.-49-276C>T		intron	N/A	ENSP00000432266.1
	YIPF1	ENST00000469457.5	TSL:3	n.270C>T		non_coding_transcript_exon	Exon 2 of 8

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 106342 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 56364

African (AFR) AF: 0.00 AC: 0 AN: 4556

American (AMR) AF: 0.00 AC: 0 AN: 5604

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3890

East Asian (EAS) AF: 0.00 AC: 0 AN: 8888

South Asian (SAS) AF: 0.00 AC: 0 AN: 9462

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4148

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 432

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 63356

Other (OTH) AF: 0.00 AC: 0 AN: 6006

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.7
DANN	Benign	0.92
PhyloP100		-0.11

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs3817871; hg19: chr1-54354935;