rs7731626

Variant names:

• chr5-56148856-G-A
• rs7731626
• NM_024669.3:c.484-4927C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-56148856-G-A
• chr5-56148856-G-C

Variant summary

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

The NM_024669.3(ANKRD55):​c.484-4927C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,738 control chromosomes in the GnomAD database, including 7,395 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 0.30 (7395 hom., cov: 30)
• Consequence: ANKRD55 NM_024669.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.770

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD55	NM_024669.3	c.484-4927C>T		intron_variant	Intron 6 of 11	ENST00000341048.9	NP_078945.2
ANKRD55	XM_047417710.1	c.-3-4927C>T		intron_variant	Intron 2 of 7		XP_047273666.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD55	ENST00000341048.9	c.484-4927C>T		intron_variant	Intron 6 of 11	2	NM_024669.3	ENSP00000342295.4
ANKRD55	ENST00000504958.6	c.483+10977C>T		intron_variant	Intron 5 of 9	5		ENSP00000424230.1
ANKRD55	ENST00000513241.2	c.397-4927C>T		intron_variant	Intron 5 of 5	5		ENSP00000423507.2
ANKRD55	ENST00000505970.2	n.254-4927C>T		intron_variant	Intron 3 of 6	3

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45396 AN: 151620 Hom.: 7396 Cov.: 30

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.299 AC: 45416 AN: 151738 Hom.: 7395 Cov.: 30 AF XY: 0.293 AC XY: 21722 AN XY: 74122

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.321

Alfa AF: 0.338 Hom.: 2426

Bravo AF: 0.301

Asia WGS AF: 0.167 AC: 581 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	1.0
DANN	Benign	0.60

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: rs7731626; hg19: chr5-55444683;