10-87843558-T-C

Variant names:

• chr10-87843558-T-C
• rs10887758
• ENST00000438248.1:n.318-252T>C

Variant summary

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

The ENST00000438248.1(CFL1P1):​n.318-252T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,086 control chromosomes in the GnomAD database, including 2,838 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 0.18 (2838 hom., cov: 32)
• Consequence: CFL1P1 ENST00000438248.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.20
• Publications: 6 publications found

Genes affected

CFL1P1 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFL1P1	NR_028492.1	n.318-252T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFL1P1	ENST00000438248.1	n.318-252T>C		intron_variant	Intron 3 of 3	1
CFL1P1	ENST00000804820.1	n.244-256T>C		intron_variant	Intron 2 of 3
CFL1P1	ENST00000804821.1	n.184-252T>C		intron_variant	Intron 2 of 3
CFL1P1	ENST00000804822.1	n.358-252T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28023 AN: 151966 Hom.: 2817 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.185 AC: 28090 AN: 152086 Hom.: 2838 Cov.: 32 AF XY: 0.186 AC XY: 13856 AN XY: 74336

African (AFR) AF: 0.128 AC: 5327 AN: 41490

American (AMR) AF: 0.232 AC: 3537 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 636 AN: 3470

East Asian (EAS) AF: 0.360 AC: 1858 AN: 5166

South Asian (SAS) AF: 0.215 AC: 1036 AN: 4820

European-Finnish (FIN) AF: 0.173 AC: 1832 AN: 10572

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13290 AN: 67982

Other (OTH) AF: 0.204 AC: 430 AN: 2110

Alfa AF: 0.187 Hom.: 3766

Bravo AF: 0.186

Asia WGS AF: 0.301 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.17
DANN	Benign	0.50
PhyloP100		-4.2

Splicing

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

Other links and lift over

dbSNP: rs10887758; hg19: chr10-89603315;