rs10887756

chr10-87837893-T-A

Variant summary

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

The NR_028492.1(CFL1P1):n.317+5641T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 151,920 control chromosomes in the GnomAD database, including 39,561 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 0.71 (39561 hom., cov: 31)
• Consequence: CFL1P1 NR_028492.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785

Genes affected

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

ATAD1 (HGNC:25903): (ATPase family AAA domain containing 1) Predicted to enable ATP binding activity and transmembrane protein dislocase activity. Involved in extraction of mislocalized protein from mitochondrial outer membrane. Located in mitochondrial outer membrane and peroxisomal membrane. Implicated in hyperekplexia 4. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFL1P1	NR_028492.1	n.317+5641T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFL1P1	ENST00000438248.1	n.317+5641T>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108441 AN: 151802 Hom.: 39528 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.714 AC: 108522 AN: 151920 Hom.: 39561 Cov.: 31 AF XY: 0.710 AC XY: 52712 AN XY: 74200

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.825

Gnomad4 ASJ AF: 0.771

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.740

Alfa AF: 0.743 Hom.: 5280

Bravo AF: 0.720

Asia WGS AF: 0.671 AC: 2334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.28
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10887756; hg19: chr10-89597650;