NM_207371.4:c.2222C>T

Variant names:

• chr10-21515601-G-A
• rs748694942
• NM_207371.4:c.2222C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_207371.4(SKIDA1):​c.2222C>T​(p.Pro741Leu) variant causes a missense change. 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P741R) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SKIDA1 NM_207371.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.88
• Publications: 0 publications found

Genes affected

SKIDA1 (HGNC:32697): (SKI/DACH domain containing 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.1441333).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207371.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SKIDA1	NM_207371.4	MANE Select	c.2222C>T	p.Pro741Leu	missense	Exon 4 of 4	NP_997254.3	Q1XH10-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SKIDA1	ENST00000449193.7	TSL:3 MANE Select	c.2222C>T	p.Pro741Leu	missense	Exon 4 of 4	ENSP00000410041.2	Q1XH10-1
	SKIDA1	ENST00000444772.3	TSL:5	c.1985C>T	p.Pro662Leu	missense	Exon 2 of 2	ENSP00000442432.1	Q1XH10-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.091
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.40
CADD	Benign	22
DANN	Uncertain	1.0
Eigen	Benign	-0.12
Eigen_PC	Benign	0.081
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.81	T
M_CAP	Benign	0.0039	T
MetaRNN	Benign	0.14	T
MetaSVM	Benign	-0.96	T
PhyloP100		3.9
PrimateAI	Uncertain	0.49	T
PROVEAN	Uncertain	-3.0	D
REVEL	Benign	0.23
Sift	Uncertain	0.012	D
Sift4G	Benign	0.088	T
Vest4		0.19
MutPred		0.18		Loss of methylation at K743 (P = 0.0545)
MVP		0.21
ClinPred		0.62	D
GERP RS		4.8
Varity_R		0.12
gMVP		0.38
Mutation Taster		=82/18	polymorphism

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

Other links and lift over

dbSNP: rs748694942; hg19: chr10-21804530;