rs10507113

Positions:

• chr12-99216760-T-A
• chr12-99216760-T-C

Variant summary

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

The NM_001352186.2(ANKS1B):​c.2419+27582A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0712 in 152,258 control chromosomes in the GnomAD database, including 805 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 0.071 (805 hom., cov: 33)
• Consequence: ANKS1B NM_001352186.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300

Genes affected

ANKS1B (HGNC:24600): (ankyrin repeat and sterile alpha motif domain containing 1B) This gene encodes a multi-domain protein that is predominantly expressed in brain and testis. This protein interacts with amyloid beta protein precursor (AbetaPP) and may have a role in normal brain development, and in the pathogenesis of Alzheimer's disease. Expression of this gene has been shown to be elevated in patients with pre-B cell acute lymphocytic leukemia associated with t(1;19) translocation. Alternatively spliced transcript variants encoding different isoforms (some with different subcellular localization, PMID:15004329) have been described for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKS1B	NM_001352186.2	c.2419+27582A>T		intron_variant		ENST00000683438.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKS1B	ENST00000683438.2	c.2419+27582A>T		intron_variant			NM_001352186.2	P1
ANKS1B	ENST00000547010.5	c.1147+27594A>T		intron_variant		1
ANKS1B	ENST00000547776.6	c.2419+27582A>T		intron_variant		1
ANKS1B	ENST00000550778.5	c.234+27582A>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0711 AC: 10811 AN: 152140 Hom.: 802 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0399

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.00339

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0712 AC: 10836 AN: 152258 Hom.: 805 Cov.: 33 AF XY: 0.0696 AC XY: 5180 AN XY: 74470

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.0398

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.00339

Gnomad4 NFE AF: 0.0128

Gnomad4 OTH AF: 0.0633

Alfa AF: 0.0396 Hom.: 61

Bravo AF: 0.0785

Asia WGS AF: 0.118 AC: 410 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.8
DANN	Benign	0.75

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: rs10507113; hg19: chr12-99610538;