20-58221728-G-A

Variant names:

• chr20-58221728-G-A
• rs4811971
• NM_001304369.2:c.562-225C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001304369.2(ANKRD60):​c.562-225C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,958 control chromosomes in the GnomAD database, including 31,274 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 0.63 (31274 hom., cov: 30)
• Consequence: ANKRD60 NM_001304369.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 15 publications found

Genes affected

ANKRD60 (HGNC:16217): (ankyrin repeat domain 60)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304369.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD60	NM_001304369.2	MANE Select	c.562-225C>T		intron	N/A	NP_001291298.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD60	ENST00000457363.2	TSL:5 MANE Select	c.562-225C>T		intron	N/A	ENSP00000396747.1

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96146 AN: 151840 Hom.: 31266 Cov.: 30

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.633 AC: 96188 AN: 151958 Hom.: 31274 Cov.: 30 AF XY: 0.636 AC XY: 47202 AN XY: 74248

African (AFR) AF: 0.475 AC: 19703 AN: 41438

American (AMR) AF: 0.768 AC: 11742 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2529 AN: 3470

East Asian (EAS) AF: 0.625 AC: 3222 AN: 5152

South Asian (SAS) AF: 0.642 AC: 3088 AN: 4812

European-Finnish (FIN) AF: 0.699 AC: 7360 AN: 10526

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46241 AN: 67960

Other (OTH) AF: 0.682 AC: 1441 AN: 2114

Alfa AF: 0.671 Hom.: 116959

Bravo AF: 0.631

Asia WGS AF: 0.609 AC: 2123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0070
DANN	Benign	0.70
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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: rs4811971; hg19: chr20-56796784; COSMIC: COSV107466390;