chr5-56105771-A-G

Position:

• chr5-56105771-A-G

Variant summary

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

The NM_024669.3(ANKRD55):​c.1631-3185T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,098 control chromosomes in the GnomAD database, including 13,454 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 0.40 (13454 hom., cov: 32)
• Consequence: ANKRD55 NM_024669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD55	NM_024669.3	c.1631-3185T>C		intron_variant		ENST00000341048.9	NP_078945.2
ANKRD55	XM_047417710.1	c.1145-3185T>C		intron_variant			XP_047273666.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD55	ENST00000341048.9	c.1631-3185T>C		intron_variant		2	NM_024669.3	ENSP00000342295	P1
	ENST00000645512.1	n.280-4782A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60454 AN: 151980 Hom.: 13435 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.398 AC: 60515 AN: 152098 Hom.: 13454 Cov.: 32 AF XY: 0.396 AC XY: 29472 AN XY: 74374

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.380

Alfa AF: 0.359 Hom.: 1431

Bravo AF: 0.400

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.58

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: rs191205; hg19: chr5-55401598; COSMIC: COSV61945157;