6-34959503-A-G

Variant names:

• chr6-34959503-A-G
• rs1535001
• NM_015245.3:c.198-7736A>G

Variant summary

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

The NM_015245.3(ANKS1A):​c.198-7736A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,112 control chromosomes in the GnomAD database, including 21,545 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 0.46 (21545 hom., cov: 32)
• Consequence: ANKS1A NM_015245.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 15 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 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.198-7736A>G		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.198-7736A>G		intron	N/A	ENSP00000353518.3
	ANKS1A	ENST00000649117.1		c.198-7736A>G		intron	N/A	ENSP00000497393.1
	ANKS1A	ENST00000650178.1		c.198-7736A>G		intron	N/A	ENSP00000497939.1

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70264 AN: 151994 Hom.: 21484 Cov.: 32

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.463 AC: 70371 AN: 152112 Hom.: 21545 Cov.: 32 AF XY: 0.461 AC XY: 34257 AN XY: 74348

African (AFR) AF: 0.852 AC: 35348 AN: 41484

American (AMR) AF: 0.392 AC: 5992 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1636 AN: 3470

East Asian (EAS) AF: 0.703 AC: 3635 AN: 5170

South Asian (SAS) AF: 0.417 AC: 2012 AN: 4822

European-Finnish (FIN) AF: 0.212 AC: 2248 AN: 10582

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18268 AN: 67982

Other (OTH) AF: 0.491 AC: 1037 AN: 2114

Alfa AF: 0.354 Hom.: 9066

Bravo AF: 0.497

Asia WGS AF: 0.550 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.0
DANN	Benign	0.56
PhyloP100		0.081
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: rs1535001; hg19: chr6-34927280;