5-56105771-A-G

Variant names:

• chr5-56105771-A-G
• rs191205
• NM_024669.3:c.1631-3185T>C

Variant summary

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

The NM_024669.3(ANKRD55):​c.1631-3185T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,098 control chromosomes in the GnomAD database, including 13,454 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 0.40 (13454 hom., cov: 32)
• Consequence: ANKRD55 NM_024669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490
• Publications: 3 publications found

Genes affected

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

ENSG00000249236 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 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.1631-3185T>C		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.1631-3185T>C		intron	N/A	ENSP00000342295.4
	ANKRD55	ENST00000434982.2	TSL:1	c.767-3185T>C		intron	N/A	ENSP00000429421.1
	ANKRD55	ENST00000504958.6	TSL:5	c.1502-3185T>C		intron	N/A	ENSP00000424230.1

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60454 AN: 151980 Hom.: 13435 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.398 AC: 60515 AN: 152098 Hom.: 13454 Cov.: 32 AF XY: 0.396 AC XY: 29472 AN XY: 74374

African (AFR) AF: 0.617 AC: 25622 AN: 41494

American (AMR) AF: 0.289 AC: 4412 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1226 AN: 3472

East Asian (EAS) AF: 0.291 AC: 1505 AN: 5164

South Asian (SAS) AF: 0.392 AC: 1888 AN: 4816

European-Finnish (FIN) AF: 0.329 AC: 3487 AN: 10592

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21154 AN: 67974

Other (OTH) AF: 0.380 AC: 800 AN: 2106

Alfa AF: 0.360 Hom.: 3285

Bravo AF: 0.400

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.58
PhyloP100		-0.49
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: rs191205; hg19: chr5-55401598; COSMIC: COSV61945157;