rs10509412

Variant names:

• chr10-87839597-A-C
• rs10509412
• ENST00000438248.1:n.318-4213A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-87839597-A-C
• chr10-87839597-A-G

Variant summary

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

The ENST00000438248.1(CFL1P1):​n.318-4213A>C variant causes a intron 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 ENST00000438248.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 7 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=-0.65).
• 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 rank	MANE	Protein	UniProt
CFL1P1	NR_028492.1	n.318-4213A>C		intron_variant	Intron 3 of 3
ATAD1	XM_005270252.6	c.-14+1590T>G		intron_variant	Intron 1 of 9		XP_005270309.1
ATAD1	XM_047425908.1	c.-163+1590T>G		intron_variant	Intron 1 of 10		XP_047281864.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFL1P1	ENST00000438248.1	n.318-4213A>C		intron_variant	Intron 3 of 3	1
ATAD1	ENST00000495903.1	c.-14+1590T>G		intron_variant	Intron 1 of 4	3		ENSP00000504881.1
ATAD1	ENST00000680388.1	n.-14+1590T>G		intron_variant	Intron 1 of 10			ENSP00000505894.1

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

African (AFR) AF: 0.137 AC: 5685 AN: 41510

American (AMR) AF: 0.355 AC: 5420 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1254 AN: 3470

East Asian (EAS) AF: 0.508 AC: 2626 AN: 5174

South Asian (SAS) AF: 0.193 AC: 929 AN: 4812

European-Finnish (FIN) AF: 0.356 AC: 3744 AN: 10530

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26860 AN: 67958

Other (OTH) AF: 0.331 AC: 700 AN: 2112

Alfa AF: 0.360 Hom.: 19439

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10509412; hg19: chr10-89599354;