5-56143024-C-T

Position:

• chr5-56143024-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.612+777G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,124 control chromosomes in the GnomAD database, including 2,095 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 0.15 (2095 hom., cov: 32)
• Consequence: ANKRD55 NM_024669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.796

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=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD55	NM_024669.3	c.612+777G>A		intron_variant		ENST00000341048.9
ANKRD55	XM_047417710.1	c.126+777G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD55	ENST00000341048.9	c.612+777G>A		intron_variant		2	NM_024669.3	P1
ANKRD55	ENST00000504958.6	c.484-15918G>A		intron_variant		5
ANKRD55	ENST00000505970.2	n.382+777G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22170 AN: 152006 Hom.: 2098 Cov.: 32

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.146 AC: 22163 AN: 152124 Hom.: 2095 Cov.: 32 AF XY: 0.142 AC XY: 10555 AN XY: 74364

Gnomad4 AFR AF: 0.0473

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.0116

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.166

Alfa AF: 0.194 Hom.: 4042

Bravo AF: 0.141

Asia WGS AF: 0.0600 AC: 210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	16
DANN	Benign	0.67

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: rs10065637; hg19: chr5-55438851;