6-34987926-C-A

Position:

• chr6-34987926-C-A

Variant summary

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

The NM_015245.3(ANKS1A):​c.1210-1298C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,194 control chromosomes in the GnomAD database, including 49,819 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 0.80 (49819 hom., cov: 33)
• Consequence: ANKS1A NM_015245.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

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

Verdict is Benign. Variant got -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 = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKS1A	NM_015245.3	c.1210-1298C>A		intron_variant		ENST00000360359.5	NP_056060.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKS1A	ENST00000360359.5	c.1210-1298C>A		intron_variant		1	NM_015245.3	ENSP00000353518
ANKS1A	ENST00000649117.1	c.1273-1298C>A		intron_variant				ENSP00000497393	P1
ANKS1A	ENST00000650178.1	c.1273-1298C>A		intron_variant				ENSP00000497939

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121499 AN: 152076 Hom.: 49779 Cov.: 33

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.799 AC: 121592 AN: 152194 Hom.: 49819 Cov.: 33 AF XY: 0.797 AC XY: 59259 AN XY: 74396

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.900

Gnomad4 OTH AF: 0.805

Alfa AF: 0.846 Hom.: 6882

Bravo AF: 0.785

Asia WGS AF: 0.755 AC: 2627 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	2.5
DANN	Benign	0.64

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: rs7740148; hg19: chr6-34955703;