rs10065637

Variant names:

• chr5-56143024-C-T
• rs10065637
• NM_024669.3:c.612+777G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 64 publications found

Genes affected

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

ENSG00000296884 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ANKRD55	NM_024669.3	c.612+777G>A		intron_variant	Intron 7 of 11	ENST00000341048.9	NP_078945.2
ANKRD55	XM_047417710.1	c.126+777G>A		intron_variant	Intron 3 of 7		XP_047273666.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD55	ENST00000341048.9	c.612+777G>A		intron_variant	Intron 7 of 11	2	NM_024669.3	ENSP00000342295.4
ANKRD55	ENST00000504958.6	c.484-15918G>A		intron_variant	Intron 5 of 9	5		ENSP00000424230.1
ANKRD55	ENST00000505970.2	n.382+777G>A		intron_variant	Intron 4 of 6	3
ENSG00000296884	ENST00000743331.1	n.131+18766C>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.0473 AC: 1965 AN: 41536

American (AMR) AF: 0.132 AC: 2025 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 949 AN: 3466

East Asian (EAS) AF: 0.0116 AC: 60 AN: 5178

South Asian (SAS) AF: 0.116 AC: 558 AN: 4812

European-Finnish (FIN) AF: 0.143 AC: 1513 AN: 10574

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14446 AN: 67946

Other (OTH) AF: 0.166 AC: 350 AN: 2112

Alfa AF: 0.185 Hom.: 9454

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
PhyloP100		0.80
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10065637; hg19: chr5-55438851;