chr4-124669219-C-G

Position:

• chr4-124669219-C-G

Variant summary

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

The NM_020337.3(ANKRD50):​c.4058G>C​(p.Gly1353Ala) 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. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ANKRD50 NM_020337.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.23

Genes affected

ANKRD50 (HGNC:29223): (ankyrin repeat domain containing 50) Involved in endocytic recycling. Predicted to be located in endosome. [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=0.13687602).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD50	NM_020337.3	c.4058G>C	p.Gly1353Ala	missense_variant	4/5	ENST00000504087.6
ANKRD50	NM_001167882.2	c.3521G>C	p.Gly1174Ala	missense_variant	3/4
ANKRD50	XM_017008471.2	c.4058G>C	p.Gly1353Ala	missense_variant	3/4
ANKRD50	XM_047415992.1	c.4058G>C	p.Gly1353Ala	missense_variant	4/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD50	ENST00000504087.6	c.4058G>C	p.Gly1353Ala	missense_variant	4/5	2	NM_020337.3	P1
ANKRD50	ENST00000515641.1	c.3521G>C	p.Gly1174Ala	missense_variant	3/4	2

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
AlphaMissense	Benign	0.074
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Benign	17
DANN	Benign	0.91
DEOGEN2	Benign	0.020	T;.
Eigen	Benign	-0.094
Eigen_PC	Benign	0.13
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Benign	0.83	T;T
M_CAP	Benign	0.0049	T
MetaRNN	Benign	0.14	T;T
MetaSVM	Benign	-0.93	T
MutationAssessor	Benign	0.34	N;.
MutationTaster	Benign	0.89	N;N
PrimateAI	Uncertain	0.57	T
PROVEAN	Benign	-0.33	N;N
REVEL	Benign	0.052
Sift	Benign	0.37	T;T
Sift4G	Benign	1.0	T;T
Polyphen		0.043	B;.
Vest4		0.39
MutPred		0.25		Gain of helix (P = 0.0425);.;
MVP		0.52
MPC		0.24
ClinPred		0.48	T
GERP RS		5.2
Varity_R		0.11
gMVP		0.074

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr4-125590374;