rs1477654

Variant names:

• chr5-99948045-C-T
• rs1477654

Variant summary

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

The variant allele was found at a frequency of 0.211 in 152,068 control chromosomes in the GnomAD database, including 3,549 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 0.21 (3549 hom., cov: 32)
• Consequence: CRLF3P2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183
• Publications: 4 publications found

Genes affected

CRLF3P2 (HGNC:54733): (CRLF3 pseudogene 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRLF3P2		n.99948045C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRLF3P2	ENST00000511386.1	n.*250G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32001 AN: 151950 Hom.: 3545 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.211 AC: 32028 AN: 152068 Hom.: 3549 Cov.: 32 AF XY: 0.205 AC XY: 15224 AN XY: 74330

African (AFR) AF: 0.163 AC: 6775 AN: 41494

American (AMR) AF: 0.185 AC: 2828 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3470

East Asian (EAS) AF: 0.115 AC: 596 AN: 5186

South Asian (SAS) AF: 0.203 AC: 978 AN: 4812

European-Finnish (FIN) AF: 0.182 AC: 1916 AN: 10556

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17641 AN: 67960

Other (OTH) AF: 0.203 AC: 428 AN: 2104

Alfa AF: 0.237 Hom.: 2115

Bravo AF: 0.204

Asia WGS AF: 0.149 AC: 519 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.2
DANN	Benign	0.84
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1477654; hg19: chr5-99283749;