ENST00000438248.1:n.317+1616T>G

Variant names:

• chr10-87833868-T-G
• rs7085791
• ENST00000438248.1:n.317+1616T>G

Variant summary

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

The ENST00000438248.1(CFL1P1):​n.317+1616T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 151,758 control chromosomes in the GnomAD database, including 47,938 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 0.79 (47938 hom., cov: 28)
• Consequence: CFL1P1 ENST00000438248.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATAD1	XM_005270252.6	c.-14+7319A>C		intron_variant	Intron 1 of 9		XP_005270309.1
ATAD1	XM_047425908.1	c.-163+7319A>C		intron_variant	Intron 1 of 10		XP_047281864.1
ATAD1	XM_047425911.1	c.-14+7319A>C		intron_variant	Intron 1 of 8		XP_047281867.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFL1P1	ENST00000438248.1	n.317+1616T>G		intron_variant	Intron 3 of 3	1
ATAD1	ENST00000495903.1	c.-14+7319A>C		intron_variant	Intron 1 of 4	3		ENSP00000504881.1
ATAD1	ENST00000680388.1	n.-14+7319A>C		intron_variant	Intron 1 of 10			ENSP00000505894.1

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120100 AN: 151640 Hom.: 47889 Cov.: 28

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.792 AC: 120208 AN: 151758 Hom.: 47938 Cov.: 28 AF XY: 0.786 AC XY: 58264 AN XY: 74172

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.845

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.803

Alfa AF: 0.723 Hom.: 2106

Bravo AF: 0.808

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.99
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7085791; hg19: chr10-89593625;