rs253414

chr5-75660692-C-T

Variant summary

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

The NM_001276713.2(ANKDD1B):c.1095+1311C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,040 control chromosomes in the GnomAD database, including 25,678 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 0.57 (25678 hom., cov: 32)
• Consequence: ANKDD1B NM_001276713.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.978

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 (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKDD1B	NM_001276713.2	c.1095+1311C>T		intron_variant		ENST00000601380.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKDD1B	ENST00000601380.4	c.1095+1311C>T		intron_variant		5	NM_001276713.2	P1

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86516 AN: 151918 Hom.: 25666 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.569 AC: 86566 AN: 152040 Hom.: 25678 Cov.: 32 AF XY: 0.563 AC XY: 41841 AN XY: 74334

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.600

Alfa AF: 0.647 Hom.: 54852

Bravo AF: 0.567

Asia WGS AF: 0.415 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.24
Dann	Benign	0.56

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: rs253414; hg19: chr5-74956517;