chr20-58228297-C-T

Variant names:

• chr20-58228297-C-T
• rs1192514
• NM_001304369.2:c.357G>A

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_001304369.2(ANKRD60):​c.357G>A​(p.Arg119Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 1,551,084 control chromosomes in the GnomAD database, including 62,922 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 0.28 (6218 hom., cov: 31)
  • Exomes 𝑓: 0.28 (56704 hom.)
• Consequence: ANKRD60 NM_001304369.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -11 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.024).
• BP7: Synonymous conserved (PhyloP=0.159 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.401 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.357G>A	p.Arg119Arg	synonymous	Exon 1 of 4	NP_001291298.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD60	ENST00000457363.2	TSL:5 MANE Select	c.357G>A	p.Arg119Arg	synonymous	Exon 1 of 4	ENSP00000396747.1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42341 AN: 151862 Hom.: 6201 Cov.: 31

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.321

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.294

GnomAD2 exomes AF: 0.327 AC: 50599 AN: 154606 AF XY: 0.331

Gnomad AFR exome AF: 0.260

Gnomad AMR exome AF: 0.449

Gnomad ASJ exome AF: 0.398

Gnomad EAS exome AF: 0.376

Gnomad FIN exome AF: 0.201

Gnomad NFE exome AF: 0.265

Gnomad OTH exome AF: 0.319

GnomAD4 exome AF: 0.279 AC: 389942 AN: 1399104 Hom.: 56704 Cov.: 36 AF XY: 0.284 AC XY: 195717 AN XY: 690068

African (AFR) AF: 0.260 AC: 8204 AN: 31598

American (AMR) AF: 0.437 AC: 15576 AN: 35682

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 9844 AN: 25180

East Asian (EAS) AF: 0.304 AC: 10868 AN: 35738

South Asian (SAS) AF: 0.421 AC: 33316 AN: 79224

European-Finnish (FIN) AF: 0.204 AC: 10005 AN: 49120

Middle Eastern (MID) AF: 0.318 AC: 1807 AN: 5688

European-Non Finnish (NFE) AF: 0.262 AC: 283058 AN: 1078870

Other (OTH) AF: 0.298 AC: 17264 AN: 58004

GnomAD4 genome AF: 0.279 AC: 42398 AN: 151980 Hom.: 6218 Cov.: 31 AF XY: 0.282 AC XY: 20935 AN XY: 74290

African (AFR) AF: 0.261 AC: 10827 AN: 41466

American (AMR) AF: 0.357 AC: 5460 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1351 AN: 3472

East Asian (EAS) AF: 0.371 AC: 1904 AN: 5134

South Asian (SAS) AF: 0.416 AC: 2001 AN: 4810

European-Finnish (FIN) AF: 0.207 AC: 2191 AN: 10588

Middle Eastern (MID) AF: 0.321 AC: 93 AN: 290

European-Non Finnish (NFE) AF: 0.262 AC: 17828 AN: 67924

Other (OTH) AF: 0.296 AC: 623 AN: 2108

Alfa AF: 0.281 Hom.: 4783

Bravo AF: 0.288

Asia WGS AF: 0.391 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	8.8
DANN	Uncertain	0.98
PhyloP100		0.16
PromoterAI		0.0092	Neutral
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: rs1192514; hg19: chr20-56803353; COSMIC: COSV61956993; COSMIC: COSV61956993;