rs771840553

Variant names:

• chr11-13009775-C-A
• rs771840553
• NM_001080521.3:c.199C>A

Your query was ambiguous. Multiple possible variants found:

• chr11-13009775-C-A
• chr11-13009775-C-G
• chr11-13009775-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001080521.3(RASSF10):​c.199C>A​(p.Pro67Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000345 in 1,450,766 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 9/13 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P67A) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: RASSF10 NM_001080521.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380

Genes affected

RASSF10 (HGNC:33984): (Ras association domain family member 10) Predicted to be involved in positive regulation of neural precursor cell proliferation and positive regulation of neurogenesis. Predicted to be located in cytosol; microtubule organizing center; and spindle pole. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.12776217).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RASSF10	NM_001080521.3	c.199C>A	p.Pro67Thr	missense_variant	Exon 1 of 1	ENST00000529419.3	NP_001073990.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RASSF10	ENST00000529419.3	c.199C>A	p.Pro67Thr	missense_variant	Exon 1 of 1	6	NM_001080521.3	ENSP00000485526.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.0000183 AC: 4 AN: 218960 Hom.: 0 AF XY: 0.0000248 AC XY: 3 AN XY: 120984

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000915

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000105

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000345 AC: 5 AN: 1450766 Hom.: 0 Cov.: 32 AF XY: 0.00000416 AC XY: 3 AN XY: 720792

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000689

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000181

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.069
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.29
CADD	Benign	14
DANN	Benign	0.90
DEOGEN2	Benign	0.010	T
FATHMM_MKL	Benign	0.55	D
LIST_S2	Benign	0.51	T
MetaRNN	Benign	0.13	T
MutationAssessor	Benign	1.2	L
PrimateAI	Uncertain	0.65	T
Sift4G	Benign	0.59	T
Polyphen		0.94	P
Vest4		0.13
MVP		0.11
GERP RS		2.4
Varity_R		0.073
gMVP		0.34

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

LitVar

Other links and lift over

dbSNP: rs771840553; hg19: chr11-13031322;