chr10-87839597-A-C

Position:

• chr10-87839597-A-C

Variant summary

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

The NR_028492.1(CFL1P1):​n.318-4213A>C 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 0.313 in 152,050 control chromosomes in the GnomAD database, including 8,579 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 0.31 (8579 hom., cov: 31)
• Consequence: CFL1P1 NR_028492.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301

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=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFL1P1	NR_028492.1	n.318-4213A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFL1P1	ENST00000438248.1	n.318-4213A>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47565 AN: 151932 Hom.: 8583 Cov.: 31

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.313 AC: 47558 AN: 152050 Hom.: 8579 Cov.: 31 AF XY: 0.310 AC XY: 23028 AN XY: 74306

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.331

Alfa AF: 0.366 Hom.: 14388

Bravo AF: 0.311

Asia WGS AF: 0.308 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	5.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509412; hg19: chr10-89599354;