chr5-56148856-G-A

Variant names:

• chr5-56148856-G-A
• rs7731626
• NM_024669.3:c.484-4927C>T

Variant summary

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

The NM_024669.3(ANKRD55):​c.484-4927C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,738 control chromosomes in the GnomAD database, including 7,395 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 (7395 hom., cov: 30)
• Consequence: ANKRD55 NM_024669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.770
• Publications: 80 publications found

Genes affected

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

ENSG00000296884 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024669.3. 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
	ANKRD55	NM_024669.3	MANE Select	c.484-4927C>T		intron	N/A	NP_078945.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD55	ENST00000341048.9	TSL:2 MANE Select	c.484-4927C>T		intron	N/A	ENSP00000342295.4
	ANKRD55	ENST00000504958.6	TSL:5	c.483+10977C>T		intron	N/A	ENSP00000424230.1
	ANKRD55	ENST00000513241.2	TSL:5	c.397-4927C>T		intron	N/A	ENSP00000423507.2

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45396 AN: 151620 Hom.: 7396 Cov.: 30

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.299 AC: 45416 AN: 151738 Hom.: 7395 Cov.: 30 AF XY: 0.293 AC XY: 21722 AN XY: 74122

African (AFR) AF: 0.191 AC: 7913 AN: 41356

American (AMR) AF: 0.327 AC: 4990 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1427 AN: 3472

East Asian (EAS) AF: 0.100 AC: 518 AN: 5162

South Asian (SAS) AF: 0.214 AC: 1026 AN: 4800

European-Finnish (FIN) AF: 0.282 AC: 2964 AN: 10494

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25483 AN: 67898

Other (OTH) AF: 0.321 AC: 676 AN: 2104

Alfa AF: 0.338 Hom.: 15977

Bravo AF: 0.301

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.0
DANN	Benign	0.60
PhyloP100		-0.77
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: rs7731626; hg19: chr5-55444683;