rs6859219

Variant names:

• chr5-56142753-C-A
• rs6859219
• NM_024669.3:c.612+1048G>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+1048G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,174 control chromosomes in the GnomAD database, including 3,006 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 0.19 (3006 hom., cov: 32)
• Consequence: ANKRD55 NM_024669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 78 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=-0.58).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD55	NM_024669.3	c.612+1048G>T		intron_variant	Intron 7 of 11	ENST00000341048.9	NP_078945.2
ANKRD55	XM_047417710.1	c.126+1048G>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+1048G>T		intron_variant	Intron 7 of 11	2	NM_024669.3	ENSP00000342295.4
ANKRD55	ENST00000504958.6	c.484-15647G>T		intron_variant	Intron 5 of 9	5		ENSP00000424230.1
ANKRD55	ENST00000505970.2	n.382+1048G>T		intron_variant	Intron 4 of 6	3
ENSG00000296884	ENST00000743331.1	n.131+18495C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29389 AN: 152056 Hom.: 3008 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.193 AC: 29394 AN: 152174 Hom.: 3006 Cov.: 32 AF XY: 0.188 AC XY: 13968 AN XY: 74374

African (AFR) AF: 0.213 AC: 8852 AN: 41498

American (AMR) AF: 0.148 AC: 2270 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 946 AN: 3466

East Asian (EAS) AF: 0.0116 AC: 60 AN: 5178

South Asian (SAS) AF: 0.117 AC: 563 AN: 4820

European-Finnish (FIN) AF: 0.143 AC: 1518 AN: 10596

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14478 AN: 67998

Other (OTH) AF: 0.193 AC: 409 AN: 2116

Alfa AF: 0.202 Hom.: 10050

Bravo AF: 0.194

Asia WGS AF: 0.0700 AC: 245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	11
DANN	Benign	0.85
PhyloP100		-0.019
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: rs6859219; hg19: chr5-55438580;