rs6859219

Positions:

• chr5-56142753-C-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ANKRD55	NM_024669.3	c.612+1048G>T		intron_variant		ENST00000341048.9	NP_078945.2
ANKRD55	XM_047417710.1	c.126+1048G>T		intron_variant			XP_047273666.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD55	ENST00000341048.9	c.612+1048G>T		intron_variant		2	NM_024669.3	ENSP00000342295	P1
ANKRD55	ENST00000504958.6	c.484-15647G>T		intron_variant		5		ENSP00000424230
ANKRD55	ENST00000505970.2	n.382+1048G>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.0116

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.193

Alfa AF: 0.205 Hom.: 3973

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs6859219; hg19: chr5-55438580;