chr6-35037307-A-C

Variant names:

• chr6-35037307-A-C
• rs13210323
• NM_015245.3:c.2011-16792A>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.2011-16792A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,084 control chromosomes in the GnomAD database, including 7,648 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 0.30 (7648 hom., cov: 32)
• Consequence: ANKS1A NM_015245.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 26 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]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.66 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015245.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKS1A	NM_015245.3	MANE Select	c.2011-16792A>C		intron	N/A	NP_056060.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKS1A	ENST00000360359.5	TSL:1 MANE Select	c.2011-16792A>C		intron	N/A	ENSP00000353518.3
	ANKS1A	ENST00000649117.1		c.2074-16792A>C		intron	N/A	ENSP00000497393.1

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46086 AN: 151966 Hom.: 7634 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.303 AC: 46133 AN: 152084 Hom.: 7648 Cov.: 32 AF XY: 0.305 AC XY: 22639 AN XY: 74330

African (AFR) AF: 0.337 AC: 13955 AN: 41462

American (AMR) AF: 0.298 AC: 4562 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1228 AN: 3470

East Asian (EAS) AF: 0.679 AC: 3512 AN: 5174

South Asian (SAS) AF: 0.350 AC: 1686 AN: 4816

European-Finnish (FIN) AF: 0.201 AC: 2129 AN: 10576

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.268 AC: 18184 AN: 67976

Other (OTH) AF: 0.331 AC: 696 AN: 2104

Alfa AF: 0.287 Hom.: 18180

Bravo AF: 0.314

Asia WGS AF: 0.492 AC: 1711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.78
PhyloP100		0.11
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: rs13210323; hg19: chr6-35005084;