NM_015245.3:c.2011-13198G>C

Variant names:

• chr6-35040901-G-C
• rs7742443
• NM_015245.3:c.2011-13198G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015245.3(ANKS1A):​c.2011-13198G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,220 control chromosomes in the GnomAD database, including 2,439 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 0.17 (2439 hom., cov: 32)
• Consequence: ANKS1A NM_015245.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992
• Publications: 10 publications found

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]

ENSG00000286550 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKS1A	NM_015245.3	c.2011-13198G>C		intron_variant	Intron 11 of 23	ENST00000360359.5	NP_056060.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKS1A	ENST00000360359.5	c.2011-13198G>C		intron_variant	Intron 11 of 23	1	NM_015245.3	ENSP00000353518.3
ANKS1A	ENST00000649117.1	c.2074-13198G>C		intron_variant	Intron 12 of 24			ENSP00000497393.1
ENSG00000286550	ENST00000660796.1	n.*215C>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25612 AN: 152102 Hom.: 2432 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.0674

Gnomad EAS AF: 0.0208

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.168 AC: 25632 AN: 152220 Hom.: 2439 Cov.: 32 AF XY: 0.164 AC XY: 12193 AN XY: 74426

African (AFR) AF: 0.112 AC: 4661 AN: 41550

American (AMR) AF: 0.170 AC: 2603 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0674 AC: 234 AN: 3472

East Asian (EAS) AF: 0.0213 AC: 110 AN: 5176

South Asian (SAS) AF: 0.140 AC: 673 AN: 4822

European-Finnish (FIN) AF: 0.191 AC: 2025 AN: 10588

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14909 AN: 67998

Other (OTH) AF: 0.129 AC: 272 AN: 2116

Alfa AF: 0.194 Hom.: 377

Bravo AF: 0.163

Asia WGS AF: 0.125 AC: 436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.26
DANN	Benign	0.61
PhyloP100		-0.99
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7742443; hg19: chr6-35008678;