rs11206237

Variant names:

• chr1-53890688-C-A
• rs11206237
• ENST00000913540.1:c.-187G>T

Variant summary

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

The ENST00000913540.1(YIPF1):​c.-187G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 452,482 control chromosomes in the GnomAD database, including 6,483 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 0.13 (1471 hom., cov: 32)
  • Exomes 𝑓: 0.17 (5012 hom.)
• Consequence: YIPF1 ENST00000913540.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000913540.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YIPF1	ENST00000913540.1		c.-187G>T		upstream_gene	N/A	ENSP00000583599.1

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19947 AN: 152058 Hom.: 1472 Cov.: 32

Gnomad AFR AF: 0.0668

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.146

GnomAD4 exome AF: 0.174 AC: 52192 AN: 300306 Hom.: 5012 AF XY: 0.179 AC XY: 30521 AN XY: 170718

African (AFR) AF: 0.0671 AC: 574 AN: 8558

American (AMR) AF: 0.222 AC: 6030 AN: 27182

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 1955 AN: 10686

East Asian (EAS) AF: 0.172 AC: 1579 AN: 9164

South Asian (SAS) AF: 0.238 AC: 14156 AN: 59588

European-Finnish (FIN) AF: 0.110 AC: 1355 AN: 12318

Middle Eastern (MID) AF: 0.231 AC: 531 AN: 2300

European-Non Finnish (NFE) AF: 0.152 AC: 23806 AN: 156448

Other (OTH) AF: 0.157 AC: 2206 AN: 14062

GnomAD4 genome AF: 0.131 AC: 19930 AN: 152176 Hom.: 1471 Cov.: 32 AF XY: 0.132 AC XY: 9813 AN XY: 74412

African (AFR) AF: 0.0666 AC: 2766 AN: 41544

American (AMR) AF: 0.177 AC: 2710 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 637 AN: 3472

East Asian (EAS) AF: 0.168 AC: 869 AN: 5174

South Asian (SAS) AF: 0.248 AC: 1194 AN: 4816

European-Finnish (FIN) AF: 0.0985 AC: 1044 AN: 10598

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10274 AN: 67980

Other (OTH) AF: 0.144 AC: 303 AN: 2110

Alfa AF: 0.118 Hom.: 325

Bravo AF: 0.132

Asia WGS AF: 0.216 AC: 752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.7
DANN	Benign	0.62
PhyloP100		1.4
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11206237; hg19: chr1-54356361; COSMIC: COSV50779094;