chr1-53854664-A-G

Variant names:

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

Variant summary

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

The NM_018982.5(YIPF1):​c.*9-2394T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.033 in 152,282 control chromosomes in the GnomAD database, including 144 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 0.033 (144 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YIPF1	NM_018982.5	c.*9-2394T>C		intron_variant	Intron 10 of 10	ENST00000072644.7	NP_061855.1
YIPF1	NR_036639.2	n.1334+337T>C		intron_variant	Intron 11 of 11
YIPF1	NR_036640.2	n.1114+337T>C		intron_variant	Intron 10 of 10
YIPF1	NR_135075.2	n.984-2394T>C		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>C		intron_variant	Intron 10 of 10	1	NM_018982.5	ENSP00000072644.1
YIPF1	ENST00000464950.6	n.*59+337T>C		intron_variant	Intron 10 of 10	1		ENSP00000432266.1
YIPF1	ENST00000371399.5	c.*9-2394T>C		intron_variant	Intron 8 of 8	2		ENSP00000360452.1

Frequencies

GnomAD3 genomes AF: 0.0330 AC: 5015 AN: 152164 Hom.: 144 Cov.: 32

Gnomad AFR AF: 0.00823

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0435

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0442

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0330 AC: 5019 AN: 152282 Hom.: 144 Cov.: 32 AF XY: 0.0334 AC XY: 2490 AN XY: 74454

African (AFR) AF: 0.00821 AC: 341 AN: 41552

American (AMR) AF: 0.0435 AC: 665 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3470

East Asian (EAS) AF: 0.117 AC: 606 AN: 5176

South Asian (SAS) AF: 0.0170 AC: 82 AN: 4826

European-Finnish (FIN) AF: 0.0107 AC: 114 AN: 10620

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0442 AC: 3004 AN: 68022

Other (OTH) AF: 0.0374 AC: 79 AN: 2114

Alfa AF: 0.0402 Hom.: 345

Bravo AF: 0.0352

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.7
DANN	Benign	0.40
PhyloP100		2.2
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: rs11206226; hg19: chr1-54320337;