rs10788569

Positions:

• chr10-87844975-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_028492.1(CFL1P1):​n.1483T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,148 control chromosomes in the GnomAD database, including 4,429 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 (4429 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: CFL1P1 NR_028492.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311

Genes affected

CFL1P1 (HGNC:28560): (cofilin 1 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFL1P1	NR_028492.1	n.1483T>C		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFL1P1	ENST00000438248.1	n.1483T>C		non_coding_transcript_exon_variant	4/4	1

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35403 AN: 152030 Hom.: 4411 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.243

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.233 AC: 35465 AN: 152148 Hom.: 4429 Cov.: 32 AF XY: 0.237 AC XY: 17600 AN XY: 74372

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.250

Alfa AF: 0.242 Hom.: 4544

Bravo AF: 0.228

Asia WGS AF: 0.327 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10788569; hg19: chr10-89604732;