rs1192514

Positions:

• chr20-58228297-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_001304369.2(ANKRD60):​c.357G>A​(p.Arg119=) 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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD60	NM_001304369.2	c.357G>A	p.Arg119=	synonymous_variant	1/4	ENST00000457363.2
ANKRD60	XM_047439902.1	c.357G>A	p.Arg119=	synonymous_variant	1/4
ANKRD60	XM_047439903.1	c.357G>A	p.Arg119=	synonymous_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD60	ENST00000457363.2	c.357G>A	p.Arg119=	synonymous_variant	1/4	5	NM_001304369.2	P1

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

GnomAD3 exomes AF: 0.327 AC: 50599 AN: 154606 Hom.: 8997 AF XY: 0.331 AC XY: 27105 AN XY: 81876

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 SAS exome AF: 0.422

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

Gnomad4 AFR exome AF: 0.260

Gnomad4 AMR exome AF: 0.437

Gnomad4 ASJ exome AF: 0.391

Gnomad4 EAS exome AF: 0.304

Gnomad4 SAS exome AF: 0.421

Gnomad4 FIN exome AF: 0.204

Gnomad4 NFE exome AF: 0.262

Gnomad4 OTH exome AF: 0.298

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

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.296

Alfa AF: 0.282 Hom.: 4352

Bravo AF: 0.288

Asia WGS AF: 0.391 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	8.8
DANN	Uncertain	0.98

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: rs1192514; hg19: chr20-56803353; COSMIC: COSV61956993; COSMIC: COSV61956993;