5-56221161-C-T

Variant names:

• chr5-56221161-C-T
• rs149140
• NM_024669.3:c.58+11695G>A

Variant summary

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

The NM_024669.3(ANKRD55):​c.58+11695G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,028 control chromosomes in the GnomAD database, including 10,856 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 0.36 (10856 hom., cov: 32)
• Consequence: ANKRD55 NM_024669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 4 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD55	NM_024669.3	c.58+11695G>A		intron_variant	Intron 2 of 11	ENST00000341048.9	NP_078945.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD55	ENST00000341048.9	c.58+11695G>A		intron_variant	Intron 2 of 11	2	NM_024669.3	ENSP00000342295.4
ANKRD55	ENST00000504958.6	c.58+11695G>A		intron_variant	Intron 1 of 9	5		ENSP00000424230.1
ANKRD55	ENST00000513241.2	c.-30+12080G>A		intron_variant	Intron 1 of 5	5		ENSP00000423507.2
ANKRD55	ENST00000519114.1	n.178+11695G>A		intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54369 AN: 151908 Hom.: 10851 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.358 AC: 54416 AN: 152028 Hom.: 10856 Cov.: 32 AF XY: 0.369 AC XY: 27431 AN XY: 74332

African (AFR) AF: 0.439 AC: 18175 AN: 41434

American (AMR) AF: 0.341 AC: 5214 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1068 AN: 3470

East Asian (EAS) AF: 0.842 AC: 4349 AN: 5168

South Asian (SAS) AF: 0.505 AC: 2436 AN: 4820

European-Finnish (FIN) AF: 0.353 AC: 3728 AN: 10568

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18326 AN: 67968

Other (OTH) AF: 0.347 AC: 733 AN: 2112

Alfa AF: 0.295 Hom.: 20102

Bravo AF: 0.356

Asia WGS AF: 0.636 AC: 2214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.21
PhyloP100		-0.54
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: rs149140; hg19: chr5-55516988; COSMIC: COSV61945557;