rs9332464

Variant names:

• chr5-75625861-G-A
• rs9332464
• NM_001276713.2:c.506G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-75625861-G-A
• chr5-75625861-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001276713.2(ANKDD1B):​c.506G>A​(p.Ser169Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 1,535,122 control chromosomes in the GnomAD database, including 45,531 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.26 (5619 hom., cov: 32)
  • Exomes 𝑓: 0.23 (39912 hom.)
• Consequence: ANKDD1B NM_001276713.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 19 publications found

Genes affected

ANKDD1B (HGNC:32525): (ankyrin repeat and death domain containing 1B) Predicted to be involved in signal transduction. [provided by Alliance of Genome Resources, Apr 2022]

ANKDD1B Gene-Disease associations (from GenCC):

• ankylosing spondylitis

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0033620894).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001276713.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKDD1B	NM_001276713.2	MANE Select	c.506G>A	p.Ser169Asn	missense	Exon 5 of 14	NP_001263642.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKDD1B	ENST00000601380.4	TSL:5 MANE Select	c.506G>A	p.Ser169Asn	missense	Exon 5 of 14	ENSP00000471417.1
	ANKDD1B	ENST00000885189.1		c.506G>A	p.Ser169Asn	missense	Exon 5 of 14	ENSP00000555248.1
	ANKDD1B	ENST00000672660.1		c.374G>A	p.Ser125Asn	missense	Exon 5 of 13	ENSP00000500535.1

Frequencies

GnomAD3 genomes AF: 0.263 AC: 40003 AN: 151918 Hom.: 5616 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.257

GnomAD2 exomes AF: 0.258 AC: 35641 AN: 138322 AF XY: 0.271

Gnomad AFR exome AF: 0.356

Gnomad AMR exome AF: 0.155

Gnomad ASJ exome AF: 0.276

Gnomad EAS exome AF: 0.326

Gnomad FIN exome AF: 0.235

Gnomad NFE exome AF: 0.212

Gnomad OTH exome AF: 0.247

GnomAD4 exome AF: 0.232 AC: 320399 AN: 1383086 Hom.: 39912 Cov.: 32 AF XY: 0.237 AC XY: 162090 AN XY: 682596

African (AFR) AF: 0.361 AC: 11397 AN: 31564

American (AMR) AF: 0.162 AC: 5773 AN: 35700

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 6973 AN: 25170

East Asian (EAS) AF: 0.349 AC: 12459 AN: 35728

South Asian (SAS) AF: 0.421 AC: 33317 AN: 79208

European-Finnish (FIN) AF: 0.235 AC: 7998 AN: 34028

Middle Eastern (MID) AF: 0.286 AC: 1631 AN: 5696

European-Non Finnish (NFE) AF: 0.210 AC: 226886 AN: 1078012

Other (OTH) AF: 0.241 AC: 13965 AN: 57980

GnomAD4 genome AF: 0.263 AC: 40030 AN: 152036 Hom.: 5619 Cov.: 32 AF XY: 0.267 AC XY: 19878 AN XY: 74332

African (AFR) AF: 0.353 AC: 14638 AN: 41450

American (AMR) AF: 0.201 AC: 3074 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3468

East Asian (EAS) AF: 0.330 AC: 1707 AN: 5172

South Asian (SAS) AF: 0.431 AC: 2078 AN: 4818

European-Finnish (FIN) AF: 0.234 AC: 2477 AN: 10568

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14243 AN: 67972

Other (OTH) AF: 0.254 AC: 534 AN: 2106

Alfa AF: 0.256 Hom.: 3700

Bravo AF: 0.260

TwinsUK AF: 0.220 AC: 814

ALSPAC AF: 0.212 AC: 817

ExAC AF: 0.292 AC: 5630

Asia WGS AF: 0.361 AC: 1252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.053
BayesDel_addAF	Benign	-0.78	T
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.3
DANN	Benign	0.26
DEOGEN2	Benign	0.0048	T
Eigen	Benign	-0.21
Eigen_PC	Benign	-0.17
FATHMM_MKL	Benign	0.010	N
LIST_S2	Benign	0.25	T
MetaRNN	Benign	0.0034	T
MutationAssessor	Benign	1.3	L
PhyloP100		1.6
PrimateAI	Benign	0.43	T
Sift4G	Benign	0.80	T
Vest4		0.045
ClinPred		0.0023	T
GERP RS		3.6
Varity_R		0.036
gMVP		0.34
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: rs9332464; hg19: chr5-74921686; COSMIC: COSV72645601;