rs6877664

chr5-56105508-G-Achr5-56105508-G-T

Variant summary

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

The NM_024669.3(ANKRD55):c.1631-2922C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,174 control chromosomes in the GnomAD database, including 3,409 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 0.12 (3409 hom., cov: 32)
• Consequence: ANKRD55 NM_024669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD55	NM_024669.3	c.1631-2922C>T		intron_variant		ENST00000341048.9
ANKRD55	XM_047417710.1	c.1145-2922C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD55	ENST00000341048.9	c.1631-2922C>T		intron_variant		2	NM_024669.3	P1
	ENST00000645512.1	n.280-5045G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17808 AN: 152056 Hom.: 3404 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0395

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.0117

Gnomad SAS AF: 0.0703

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00128

Gnomad OTH AF: 0.0809

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

GnomAD4 genome AF: 0.117 AC: 17844 AN: 152174 Hom.: 3409 Cov.: 32 AF XY: 0.114 AC XY: 8471 AN XY: 74410

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.0394

Gnomad4 ASJ AF: 0.00231

Gnomad4 EAS AF: 0.0118

Gnomad4 SAS AF: 0.0689

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00128

Gnomad4 OTH AF: 0.0862

Alfa AF: 0.0129 Hom.: 554

Bravo AF: 0.130

Asia WGS AF: 0.0900 AC: 314 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	0.14
Dann	Benign	0.38

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: rs6877664; hg19: chr5-55401335;