rs7717355

Variant names:

• chr5-75656076-G-A
• rs7717355
• NM_001276713.2:c.945G>A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001276713.2(ANKDD1B):​c.945G>A​(p.Thr315Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 1,526,186 control chromosomes in the GnomAD database, including 9,935 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 0.11 (1044 hom., cov: 32)
  • Exomes 𝑓: 0.11 (8891 hom.)
• Consequence: ANKDD1B NM_001276713.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.53

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP7: Synonymous conserved (PhyloP=-5.53 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKDD1B	NM_001276713.2	c.945G>A	p.Thr315Thr	synonymous_variant	Exon 9 of 14	ENST00000601380.4	NP_001263642.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKDD1B	ENST00000601380.4	c.945G>A	p.Thr315Thr	synonymous_variant	Exon 9 of 14	5	NM_001276713.2	ENSP00000471417.1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16550 AN: 151960 Hom.: 1044 Cov.: 32

Gnomad AFR AF: 0.0731

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0971

Gnomad OTH AF: 0.115

GnomAD3 exomes AF: 0.139 AC: 19094 AN: 137416 Hom.: 1615 AF XY: 0.137 AC XY: 10138 AN XY: 74248

Gnomad AFR exome AF: 0.0700

Gnomad AMR exome AF: 0.176

Gnomad ASJ exome AF: 0.167

Gnomad EAS exome AF: 0.306

Gnomad SAS exome AF: 0.140

Gnomad FIN exome AF: 0.121

Gnomad NFE exome AF: 0.0983

Gnomad OTH exome AF: 0.128

GnomAD4 exome AF: 0.107 AC: 146425 AN: 1374108 Hom.: 8891 Cov.: 26 AF XY: 0.108 AC XY: 72994 AN XY: 678520

Gnomad4 AFR exome AF: 0.0732

Gnomad4 AMR exome AF: 0.173

Gnomad4 ASJ exome AF: 0.177

Gnomad4 EAS exome AF: 0.277

Gnomad4 SAS exome AF: 0.141

Gnomad4 FIN exome AF: 0.118

Gnomad4 NFE exome AF: 0.0942

Gnomad4 OTH exome AF: 0.120

GnomAD4 genome AF: 0.109 AC: 16557 AN: 152078 Hom.: 1044 Cov.: 32 AF XY: 0.114 AC XY: 8450 AN XY: 74346

Gnomad4 AFR AF: 0.0729

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.0970

Gnomad4 OTH AF: 0.117

Alfa AF: 0.108 Hom.: 1353

Bravo AF: 0.110

Asia WGS AF: 0.210 AC: 730 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	0.45
DANN	Benign	0.38

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.13		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: rs7717355; hg19: chr5-74951901; COSMIC: COSV72645205;