5-56148213-C-T

Position:

• chr5-56148213-C-T

Variant summary

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

The NM_024669.3(ANKRD55):​c.484-4284G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 152,084 control chromosomes in the GnomAD database, including 36,941 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 0.69 (36941 hom., cov: 32)
• Consequence: ANKRD55 NM_024669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.706

Genes affected

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

ANKRD55 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD55	NM_024669.3	c.484-4284G>A		intron_variant		ENST00000341048.9	NP_078945.2
ANKRD55	XM_047417710.1	c.-3-4284G>A		intron_variant			XP_047273666.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD55	ENST00000341048.9	c.484-4284G>A		intron_variant		2	NM_024669.3	ENSP00000342295.4
ANKRD55	ENST00000504958.6	c.483+11620G>A		intron_variant		5		ENSP00000424230.1
ANKRD55	ENST00000513241.2	c.397-4284G>A		intron_variant		5		ENSP00000423507.2
ANKRD55	ENST00000505970.2	n.254-4284G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105466 AN: 151966 Hom.: 36918 Cov.: 32

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.694 AC: 105534 AN: 152084 Hom.: 36941 Cov.: 32 AF XY: 0.687 AC XY: 51099 AN XY: 74362

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.694

Alfa AF: 0.716 Hom.: 53689

Bravo AF: 0.691

Asia WGS AF: 0.534 AC: 1861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.4
DANN	Benign	0.54

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: rs10214316; hg19: chr5-55444040;