rs9332464

chr5-75625861-G-Achr5-75625861-G-C

Variant summary

Our verdict is Benign. Variant got -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. 11/15 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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKDD1B	NM_001276713.2	c.506G>A	p.Ser169Asn	missense_variant	5/14	ENST00000601380.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKDD1B	ENST00000601380.4	c.506G>A	p.Ser169Asn	missense_variant	5/14	5	NM_001276713.2	P1

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

GnomAD3 exomes AF: 0.258 AC: 35641 AN: 138322 Hom.: 5261 AF XY: 0.271 AC XY: 20268 AN XY: 74810

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 SAS exome AF: 0.422

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

Gnomad4 AFR exome AF: 0.361

Gnomad4 AMR exome AF: 0.162

Gnomad4 ASJ exome AF: 0.277

Gnomad4 EAS exome AF: 0.349

Gnomad4 SAS exome AF: 0.421

Gnomad4 FIN exome AF: 0.235

Gnomad4 NFE exome AF: 0.210

Gnomad4 OTH exome AF: 0.241

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

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.254

Alfa AF: 0.240 Hom.: 1912

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 v4.3

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
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

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: rs9332464; hg19: chr5-74921686; COSMIC: COSV72645601;