1-53854664-A-C

Variant names:

• chr1-53854664-A-C
• rs11206226
• NM_018982.5:c.*9-2394T>G

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.*9-2394T>G variant causes a intron 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: 32)
• Consequence: YIPF1 NM_018982.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21
• Publications: 13 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=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YIPF1	NM_018982.5	c.*9-2394T>G		intron_variant	Intron 10 of 10	ENST00000072644.7	NP_061855.1
YIPF1	NR_036639.2	n.1334+337T>G		intron_variant	Intron 11 of 11
YIPF1	NR_036640.2	n.1114+337T>G		intron_variant	Intron 10 of 10
YIPF1	NR_135075.2	n.984-2394T>G		intron_variant	Intron 8 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YIPF1	ENST00000072644.7	c.*9-2394T>G		intron_variant	Intron 10 of 10	1	NM_018982.5	ENSP00000072644.1
YIPF1	ENST00000464950.6	n.*59+337T>G		intron_variant	Intron 10 of 10	1		ENSP00000432266.1
YIPF1	ENST00000371399.5	c.*9-2394T>G		intron_variant	Intron 8 of 8	2		ENSP00000360452.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.4
DANN	Benign	0.39
PhyloP100		2.2

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: rs11206226; hg19: chr1-54320337;