5-56211219-A-C

Position:

• chr5-56211219-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024669.3(ANKRD55):​c.58+21637T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,030 control chromosomes in the GnomAD database, including 12,094 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 0.37 (12094 hom., cov: 32)
• Consequence: ANKRD55 NM_024669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD55	NM_024669.3	c.58+21637T>G		intron_variant		ENST00000341048.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD55	ENST00000341048.9	c.58+21637T>G		intron_variant		2	NM_024669.3	P1
ANKRD55	ENST00000504958.6	c.58+21637T>G		intron_variant		5
ANKRD55	ENST00000513241.2	c.-30+22022T>G		intron_variant		5
ANKRD55	ENST00000519114.1	n.178+21637T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56943 AN: 151912 Hom.: 12085 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.375 AC: 56996 AN: 152030 Hom.: 12094 Cov.: 32 AF XY: 0.381 AC XY: 28276 AN XY: 74306

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.351

Alfa AF: 0.269 Hom.: 5353

Bravo AF: 0.378

Asia WGS AF: 0.524 AC: 1821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.82
DANN	Benign	0.56

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: rs159572; hg19: chr5-55507046; COSMIC: COSV61945497;