rs6881896

chr5-56176728-C-T

Variant summary

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

The NM_024669.3(ANKRD55):c.182-446G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,162 control chromosomes in the GnomAD database, including 12,158 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 0.30 (12158 hom., cov: 32)
• Consequence: ANKRD55 NM_024669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490

Genes affected

ANKRD55 (HGNC:25681): (ankyrin repeat domain 55)

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 = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD55	NM_024669.3	c.182-446G>A		intron_variant		ENST00000341048.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD55	ENST00000341048.9	c.182-446G>A		intron_variant		2	NM_024669.3	P1
ANKRD55	ENST00000504958.6	c.182-446G>A		intron_variant		5
ANKRD55	ENST00000513241.2	c.95-446G>A		intron_variant		5
ANKRD55	ENST00000519114.1	n.302-446G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45309 AN: 152044 Hom.: 12115 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.298 AC: 45405 AN: 152162 Hom.: 12158 Cov.: 32 AF XY: 0.296 AC XY: 22046 AN XY: 74396

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.238

Alfa AF: 0.260 Hom.: 2065

Bravo AF: 0.321

Asia WGS AF: 0.358 AC: 1247 AN: 3478

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	0.67

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: rs6881896; hg19: chr5-55472555;