rs10761482

Positions:

• chr10-60325579-T-C

Variant summary

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

The NM_020987.5(ANK3):​c.115-45940A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 151,992 control chromosomes in the GnomAD database, including 38,780 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 0.71 (38780 hom., cov: 31)
• Consequence: ANK3 NM_020987.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

Genes affected

ANK3 (HGNC:494): (ankyrin 3) Ankyrins are a family of proteins that are believed to link the integral membrane proteins to the underlying spectrin-actin cytoskeleton and play key roles in activities such as cell motility, activation, proliferation, contact, and the maintenance of specialized membrane domains. Multiple isoforms of ankyrin with different affinities for various target proteins are expressed in a tissue-specific, developmentally regulated manner. Most ankyrins are typically composed of three structural domains: an amino-terminal domain containing multiple ankyrin repeats; a central region with a highly conserved spectrin binding domain; and a carboxy-terminal regulatory domain which is the least conserved and subject to variation. Ankyrin 3 is an immunologically distinct gene product from ankyrins 1 and 2, and was originally found at the axonal initial segment and nodes of Ranvier of neurons in the central and peripheral nervous systems. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANK3	NM_020987.5	c.115-45940A>G		intron_variant		ENST00000280772.7	NP_066267.2
ANK3	NM_001204404.2	c.64-45940A>G		intron_variant			NP_001191333.1
ANK3	NM_001320874.2	c.115-45940A>G		intron_variant			NP_001307803.1
ANK3	NM_001204403.2	c.97-45940A>G		intron_variant			NP_001191332.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANK3	ENST00000280772.7	c.115-45940A>G		intron_variant		1	NM_020987.5	ENSP00000280772.1

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107675 AN: 151874 Hom.: 38765 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.709 AC: 107730 AN: 151992 Hom.: 38780 Cov.: 31 AF XY: 0.712 AC XY: 52865 AN XY: 74290

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.904

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.739

Alfa AF: 0.759 Hom.: 70552

Bravo AF: 0.699

Asia WGS AF: 0.777 AC: 2699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.51

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: rs10761482; hg19: chr10-62085337;