chr10-60540625-A-G

Position:

• chr10-60540625-A-G

Variant summary

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

The ENST00000373827.6(ANK3):​c.96+74561T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.088 in 151,918 control chromosomes in the GnomAD database, including 1,147 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 0.088 (1147 hom., cov: 32)
• Consequence: ANK3 ENST00000373827.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANK3	NM_001204403.2	c.96+74561T>C		intron_variant			NP_001191332.1
ANK3	NM_001204404.2	c.63+31840T>C		intron_variant			NP_001191333.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANK3	ENST00000373827.6	c.96+74561T>C		intron_variant		1		ENSP00000362933
ANK3	ENST00000503366.6	c.63+31840T>C		intron_variant		2		ENSP00000425236
ANK3	ENST00000622427.4	c.63+31840T>C		intron_variant, NMD_transcript_variant		2		ENSP00000483244
ANK3	ENST00000510382.1	n.102-32000T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0880 AC: 13363 AN: 151800 Hom.: 1142 Cov.: 32

Gnomad AFR AF: 0.0168

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.0785

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0687

Gnomad OTH AF: 0.0803

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

GnomAD4 genome AF: 0.0880 AC: 13368 AN: 151918 Hom.: 1147 Cov.: 32 AF XY: 0.0980 AC XY: 7277 AN XY: 74250

Gnomad4 AFR AF: 0.0167

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.0785

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.0687

Gnomad4 OTH AF: 0.0814

Alfa AF: 0.0950 Hom.: 754

Bravo AF: 0.0884

Asia WGS AF: 0.248 AC: 860 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.49
DANN	Benign	0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1938526; hg19: chr10-62300383;