rs7742443

chr6-35040901-G-C

Variant summary

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

The NM_015245.3(ANKS1A):c.2011-13198G>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

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 = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKS1A	NM_015245.3	c.2011-13198G>C		intron_variant		ENST00000360359.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKS1A	ENST00000360359.5	c.2011-13198G>C		intron_variant		1	NM_015245.3
ANKS1A	ENST00000649117.1	c.2074-13198G>C		intron_variant				P1

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

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.0674

Gnomad4 EAS AF: 0.0213

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.129

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

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: rs7742443; hg19: chr6-35008678;