rs847851

Variant names:

• chr6-34936807-G-A
• rs847851
• NM_015245.3:c.198-30432G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-34936807-G-A
• chr6-34936807-G-C
• chr6-34936807-G-T

Variant summary

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

The NM_015245.3(ANKS1A):​c.198-30432G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 152,062 control chromosomes in the GnomAD database, including 21,510 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 (21510 hom., cov: 32)
• Consequence: ANKS1A NM_015245.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• 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 = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKS1A	NM_015245.3	c.198-30432G>A		intron_variant	Intron 1 of 23	ENST00000360359.5	NP_056060.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKS1A	ENST00000360359.5	c.198-30432G>A		intron_variant	Intron 1 of 23	1	NM_015245.3	ENSP00000353518.3
ANKS1A	ENST00000649117.1	c.198-30432G>A		intron_variant	Intron 1 of 24			ENSP00000497393.1
ANKS1A	ENST00000650178.1	c.198-30432G>A		intron_variant	Intron 1 of 9			ENSP00000497939.1

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70199 AN: 151944 Hom.: 21449 Cov.: 32

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.0659

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.462 AC: 70306 AN: 152062 Hom.: 21510 Cov.: 32 AF XY: 0.461 AC XY: 34248 AN XY: 74318

African (AFR) AF: 0.852 AC: 35352 AN: 41508

American (AMR) AF: 0.392 AC: 5984 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1627 AN: 3468

East Asian (EAS) AF: 0.702 AC: 3627 AN: 5166

South Asian (SAS) AF: 0.415 AC: 2000 AN: 4816

European-Finnish (FIN) AF: 0.213 AC: 2250 AN: 10574

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.268 AC: 18237 AN: 67952

Other (OTH) AF: 0.491 AC: 1039 AN: 2114

Alfa AF: 0.348 Hom.: 36821

Bravo AF: 0.496

Asia WGS AF: 0.546 AC: 1897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.28
PhyloP100		-0.056
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: rs847851; hg19: chr6-34904584;