ENST00000438248.1:n.317+5641T>A

Variant names:

• chr10-87837893-T-A
• rs10887756
• ENST00000438248.1:n.317+5641T>A

Variant summary

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

The ENST00000438248.1(CFL1P1):​n.317+5641T>A variant causes a intron 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 ENST00000438248.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785
• Publications: 0 publications found

Genes affected

CFL1P1 (HGNC:):

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]

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438248.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFL1P1	NR_028492.1		n.317+5641T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFL1P1	ENST00000438248.1	TSL:1	n.317+5641T>A		intron	N/A
	ATAD1	ENST00000495903.1	TSL:3	c.-14+3294A>T		intron	N/A	ENSP00000504881.1
	ATAD1	ENST00000680388.1		n.-14+3294A>T		intron	N/A	ENSP00000505894.1

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

African (AFR) AF: 0.583 AC: 24117 AN: 41402

American (AMR) AF: 0.825 AC: 12595 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2674 AN: 3470

East Asian (EAS) AF: 0.575 AC: 2965 AN: 5160

South Asian (SAS) AF: 0.639 AC: 3068 AN: 4798

European-Finnish (FIN) AF: 0.706 AC: 7433 AN: 10530

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.784 AC: 53278 AN: 67978

Other (OTH) AF: 0.740 AC: 1559 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.28
DANN	Benign	0.34
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs10887756; hg19: chr10-89597650;