5-56139393-C-T

Variant names:

• chr5-56139393-C-T
• rs10040327
• NM_024669.3:c.612+4408G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_024669.3(ANKRD55):​c.612+4408G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD55	NM_024669.3	c.612+4408G>A		intron_variant	Intron 7 of 11	ENST00000341048.9	NP_078945.2
ANKRD55	XM_047417710.1	c.126+4408G>A		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>A		intron_variant	Intron 7 of 11	2	NM_024669.3	ENSP00000342295.4
ANKRD55	ENST00000504958.6	c.484-12287G>A		intron_variant	Intron 5 of 9	5		ENSP00000424230.1
ANKRD55	ENST00000505970.2	n.382+4408G>A		intron_variant	Intron 4 of 6	3
ENSG00000296884	ENST00000743331.1	n.131+15135C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1827

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.54
PhyloP100		0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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;