rs4700060

Variant names:

• chr5-56214829-C-T
• rs4700060
• NM_024669.3:c.58+18027G>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+18027G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.088 in 152,268 control chromosomes in the GnomAD database, including 820 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 0.088 (820 hom., cov: 32)
• Consequence: ANKRD55 NM_024669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 11 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD55	NM_024669.3	c.58+18027G>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+18027G>A		intron_variant	Intron 2 of 11	2	NM_024669.3	ENSP00000342295.4
ANKRD55	ENST00000504958.6	c.58+18027G>A		intron_variant	Intron 1 of 9	5		ENSP00000424230.1
ANKRD55	ENST00000513241.2	c.-30+18412G>A		intron_variant	Intron 1 of 5	5		ENSP00000423507.2
ANKRD55	ENST00000519114.1	n.178+18027G>A		intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes AF: 0.0880 AC: 13396 AN: 152150 Hom.: 817 Cov.: 32

Gnomad AFR AF: 0.0219

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.0876

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.0880 AC: 13400 AN: 152268 Hom.: 820 Cov.: 32 AF XY: 0.0893 AC XY: 6649 AN XY: 74456

African (AFR) AF: 0.0218 AC: 907 AN: 41572

American (AMR) AF: 0.145 AC: 2217 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3470

East Asian (EAS) AF: 0.0878 AC: 455 AN: 5180

South Asian (SAS) AF: 0.124 AC: 598 AN: 4828

European-Finnish (FIN) AF: 0.129 AC: 1370 AN: 10598

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7257 AN: 68004

Other (OTH) AF: 0.0875 AC: 185 AN: 2114

Alfa AF: 0.0999 Hom.: 2396

Bravo AF: 0.0881

Asia WGS AF: 0.115 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.3
DANN	Benign	0.44
PhyloP100		0.45
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: rs4700060; hg19: chr5-55510656;