1-53889262-G-C

Variant names:

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

Variant summary

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

The NM_018982.5(YIPF1):​c.-68C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 258,242 control chromosomes in the GnomAD database, including 6,915 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 0.23 (4203 hom., cov: 33)
  • Exomes 𝑓: 0.22 (2712 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YIPF1	NM_018982.5	c.-68C>G		5_prime_UTR_variant	Exon 2 of 11	ENST00000072644.7	NP_061855.1
YIPF1	NR_036639.2	n.287C>G		non_coding_transcript_exon_variant	Exon 2 of 12
YIPF1	NR_036640.2	n.86-276C>G		intron_variant	Intron 1 of 10
YIPF1	NR_135075.2	n.85+451C>G		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
YIPF1	ENST00000072644.7	c.-68C>G		5_prime_UTR_variant	Exon 2 of 11	1	NM_018982.5	ENSP00000072644.1

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34685 AN: 152086 Hom.: 4197 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.221

GnomAD4 exome AF: 0.219 AC: 23269 AN: 106036 Hom.: 2712 Cov.: 0 AF XY: 0.221 AC XY: 12414 AN XY: 56210

African (AFR) AF: 0.286 AC: 1301 AN: 4542

American (AMR) AF: 0.252 AC: 1405 AN: 5582

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 845 AN: 3870

East Asian (EAS) AF: 0.313 AC: 2776 AN: 8862

South Asian (SAS) AF: 0.252 AC: 2383 AN: 9438

European-Finnish (FIN) AF: 0.116 AC: 482 AN: 4140

Middle Eastern (MID) AF: 0.252 AC: 109 AN: 432

European-Non Finnish (NFE) AF: 0.200 AC: 12651 AN: 63188

Other (OTH) AF: 0.220 AC: 1317 AN: 5982

GnomAD4 genome AF: 0.228 AC: 34705 AN: 152206 Hom.: 4203 Cov.: 33 AF XY: 0.228 AC XY: 16935 AN XY: 74420

African (AFR) AF: 0.298 AC: 12353 AN: 41504

American (AMR) AF: 0.244 AC: 3722 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 763 AN: 3468

East Asian (EAS) AF: 0.286 AC: 1480 AN: 5174

South Asian (SAS) AF: 0.266 AC: 1284 AN: 4832

European-Finnish (FIN) AF: 0.109 AC: 1162 AN: 10618

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13325 AN: 68010

Other (OTH) AF: 0.219 AC: 463 AN: 2114

Alfa AF: 0.213 Hom.: 485

Bravo AF: 0.240

Asia WGS AF: 0.278 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.3
DANN	Benign	0.57
PhyloP100		-0.11
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: rs3817871; hg19: chr1-54354935;