rs2820223

chr6-35041518-T-C

Variant summary

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

The NM_015245.3(ANKS1A):c.2011-12581T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,092 control chromosomes in the GnomAD database, including 13,846 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 0.38 (13846 hom., cov: 32)
• Consequence: ANKS1A NM_015245.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

Genes affected

ANKS1A (HGNC:20961): (ankyrin repeat and sterile alpha motif domain containing 1A) Predicted to enable ephrin receptor binding activity. Predicted to be involved in ephrin receptor signaling pathway; neuron remodeling; and substrate-dependent cell migration. Predicted to act upstream of or within negative regulation of ubiquitin-dependent protein catabolic process and regulation of ephrin receptor signaling pathway. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKS1A	NM_015245.3	c.2011-12581T>C		intron_variant		ENST00000360359.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKS1A	ENST00000360359.5	c.2011-12581T>C		intron_variant		1	NM_015245.3
	ENST00000660796.1	n.569A>G		non_coding_transcript_exon_variant	2/2
ANKS1A	ENST00000649117.1	c.2074-12581T>C		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58375 AN: 151974 Hom.: 13842 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.384 AC: 58362 AN: 152092 Hom.: 13846 Cov.: 32 AF XY: 0.390 AC XY: 28976 AN XY: 74352

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.380

Alfa AF: 0.448 Hom.: 2907

Bravo AF: 0.359

Asia WGS AF: 0.323 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.3
Dann	Benign	0.79

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: rs2820223; hg19: chr6-35009295;