5-56139393-C-A

Variant names:

• chr5-56139393-C-A
• rs10040327
• NM_024669.3:c.612+4408G>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.612+4408G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0997 in 152,122 control chromosomes in the GnomAD database, including 802 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 0.10 (802 hom., cov: 32)
• Consequence: ANKRD55 NM_024669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425
• Publications: 10 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD55	NM_024669.3	c.612+4408G>T		intron_variant	Intron 7 of 11	ENST00000341048.9	NP_078945.2
ANKRD55	XM_047417710.1	c.126+4408G>T		intron_variant	Intron 3 of 7		XP_047273666.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD55	ENST00000341048.9	c.612+4408G>T		intron_variant	Intron 7 of 11	2	NM_024669.3	ENSP00000342295.4
ANKRD55	ENST00000504958.6	c.484-12287G>T		intron_variant	Intron 5 of 9	5		ENSP00000424230.1
ANKRD55	ENST00000505970.2	n.382+4408G>T		intron_variant	Intron 4 of 6	3
ENSG00000296884	ENST00000743331.1	n.131+15135C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0998 AC: 15169 AN: 152004 Hom.: 802 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0686

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0305

Gnomad FIN AF: 0.0675

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0997 AC: 15169 AN: 152122 Hom.: 802 Cov.: 32 AF XY: 0.0958 AC XY: 7124 AN XY: 74364

African (AFR) AF: 0.110 AC: 4572 AN: 41500

American (AMR) AF: 0.0685 AC: 1046 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 430 AN: 3472

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5176

South Asian (SAS) AF: 0.0307 AC: 148 AN: 4814

European-Finnish (FIN) AF: 0.0675 AC: 715 AN: 10598

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7873 AN: 67974

Other (OTH) AF: 0.102 AC: 215 AN: 2108

Alfa AF: 0.108 Hom.: 1827

Bravo AF: 0.101

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.51
PhyloP100		0.42
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: rs10040327; hg19: chr5-55435220;