rs1495127

chr4-124668002-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020337.3(ANKRD50):c.*4-488G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,650 control chromosomes in the GnomAD database, including 4,401 homozygotes. 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: 𝑓 0.23 (4401 hom., cov: 32)
• Consequence: ANKRD50 NM_020337.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD50	NM_020337.3	c.*4-488G>A		intron_variant		ENST00000504087.6
ANKRD50	NM_001167882.2	c.*4-488G>A		intron_variant
ANKRD50	XM_017008471.2	c.*4-488G>A		intron_variant
ANKRD50	XM_047415992.1	c.*4-488G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD50	ENST00000504087.6	c.*4-488G>A		intron_variant		2	NM_020337.3	P1
ANKRD50	ENST00000515641.1	c.*4-488G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35493 AN: 151532 Hom.: 4404 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.206

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.234 AC: 35506 AN: 151650 Hom.: 4401 Cov.: 32 AF XY: 0.236 AC XY: 17481 AN XY: 74126

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.203

Alfa AF: 0.214 Hom.: 563

Bravo AF: 0.236

Asia WGS AF: 0.243 AC: 839 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.9
Dann	Benign	0.19

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: rs1495127; hg19: chr4-125589157;