dbSNP rs7085791: CFL1P1:n.317+1616T>A (chr10-87833868-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000495903.1(ATAD1):c.-14+7319A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000494 in 151,828 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00049 ( 0 hom., cov: 28)

Consequence

ATAD1
ENST00000495903.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.65

Variant links:

Genes affected

CFL1P1 (HGNC:):

CFL1P1 links:

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]

ATAD1 links:

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

CFL1P1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
ATAD1	XM_005270252.6 link	c.-14+7319A>T	intron_variant	Intron 1 of 9	XP_005270309.1	Q8NBU5-1
ATAD1	XM_047425908.1 link	c.-163+7319A>T	intron_variant	Intron 1 of 10	XP_047281864.1
ATAD1	XM_047425911.1 link	c.-14+7319A>T	intron_variant	Intron 1 of 8	XP_047281867.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
CFL1P1	ENST00000438248.1 link	n.317+1616T>A	intron_variant	Intron 3 of 3	1
ATAD1	ENST00000495903.1 link	c.-14+7319A>T	intron_variant	Intron 1 of 4	3	ENSP00000504881.1	A0A7P0T7Z9
ATAD1	ENST00000680388.1 link	n.-14+7319A>T	intron_variant	Intron 1 of 10		ENSP00000505894.1	A0A7P0T9U2

Frequencies

GnomAD3 genomes

AF:

0.000488

AC:

AN:

151710

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00165

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000328

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.000478

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

GnomAD4 genome

AF:

0.000494

AC:

AN:

151828

Hom.:

Cov.:

AF XY:

0.000472

AC XY:

AN XY:

74210

show subpopulations

Gnomad4 AFR

AF:

0.00167

Gnomad4 AMR

AF:

0.000328

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.000473

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.0

DANN

Benign

0.13

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over