Genetic Variant RASL10A:c.*195G>A (chr22-29313106-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_006477.5(RASL10A):c.*195G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000211 in 474,276 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: not found (cov: 33)

Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

RASL10A
NM_006477.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.438

Publications

0 publications found

Variant links:

Genes affected

RASL10A (HGNC:16954): (RAS like family 10 member A) Predicted to enable GTPase activity. Predicted to be involved in small GTPase mediated signal transduction. Predicted to be located in nucleolus and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

RASL10A links:

ENSG00000301612 (HGNC:):

ENSG00000301612 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006477.5. 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
	RASL10A	NM_006477.5	MANE Select	c.*195G>A		3_prime_UTR	Exon 3 of 3	NP_006468.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
RASL10A	ENST00000216101.7	TSL:1 MANE Select	c.*195G>A	3_prime_UTR	Exon 3 of 3	ENSP00000216101.6
RASL10A	ENST00000401450.3	TSL:2	c.*753G>A	3_prime_UTR	Exon 2 of 2	ENSP00000386095.3
ENSG00000301612	ENST00000780180.1		n.117+2759G>A	intron	N/A

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000211

AC:

AN:

474276

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

240480

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

10186

American (AMR)

AF:

0.00

AC:

AN:

11676

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11894

East Asian (EAS)

AF:

0.00

AC:

AN:

26022

South Asian (SAS)

AF:

0.00

AC:

AN:

25766

European-Finnish (FIN)

AF:

0.00

AC:

AN:

27380

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1912

European-Non Finnish (NFE)

AF:

0.00000300

AC:

AN:

333814

Other (OTH)

AF:

0.00

AC:

AN:

25626

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

6.7

(source)

DANN

Benign

0.66

PhyloP100

-0.44

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over