rs868421855

Variant names:

• chr2-16565694-G-A
• rs868421855
• NM_030797.4:c.144C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-16565694-G-A
• chr2-16565694-G-C

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_030797.4(CYRIA):​c.144C>T​(p.Ile48Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 32)
• Consequence: CYRIA NM_030797.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.30

Genes affected

CYRIA (HGNC:25373): (CYFIP related Rac1 interactor A) Predicted to enable small GTPase binding activity. Predicted to be involved in regulation of actin filament polymerization. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BP7: Synonymous conserved (PhyloP=2.3 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYRIA	NM_030797.4	c.144C>T	p.Ile48Ile	synonymous_variant	Exon 4 of 12	ENST00000381323.7	NP_110424.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYRIA	ENST00000381323.7	c.144C>T	p.Ile48Ile	synonymous_variant	Exon 4 of 12	1	NM_030797.4	ENSP00000370724.3
CYRIA	ENST00000406434.5	c.144C>T	p.Ile48Ile	synonymous_variant	Exon 5 of 13	5		ENSP00000384771.1
CYRIA	ENST00000445605.5	c.144C>T	p.Ile48Ile	synonymous_variant	Exon 4 of 5	4		ENSP00000392154.1
CYRIA	ENST00000451689.1	c.144C>T	p.Ile48Ile	synonymous_variant	Exon 5 of 6	4		ENSP00000388979.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	11
DANN	Benign	0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs868421855; hg19: chr2-16746962;