rs2513046

Variant names:

• chr11-62468622-A-G
• rs2513046
• ENST00000257247.11:c.442+23110T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-62468622-A-G
• chr11-62468622-A-T

Variant summary

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

The ENST00000257247.11(AHNAK):​c.442+23110T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 152,062 control chromosomes in the GnomAD database, including 57,967 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 0.87 (57967 hom., cov: 29)
• Consequence: AHNAK ENST00000257247.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 2 publications found

Genes affected

AHNAK (HGNC:347): (AHNAK nucleoprotein) The protein encoded by this gene is a large (700 kDa) structural scaffold protein consisting of a central domain with 128 aa repeats. The encoded protein may play a role in such diverse processes as blood-brain barrier formation, cell structure and migration, cardiac calcium channel regulation, and tumor metastasis. A much shorter variant encoding a 17 kDa isoform exists for this gene, and the shorter isoform initiates a feedback loop that regulates alternative splicing of this gene. [provided by RefSeq, Oct 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000257247.11. 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
	AHNAK	NM_024060.4		c.442+23110T>C		intron	N/A	NP_076965.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHNAK	ENST00000257247.11	TSL:1	c.442+23110T>C		intron	N/A	ENSP00000257247.7
	AHNAK	ENST00000530124.5	TSL:3	c.343-34731T>C		intron	N/A	ENSP00000433789.1
	AHNAK	ENST00000525875.1	TSL:3	n.448+23110T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.870 AC: 132242 AN: 151944 Hom.: 57929 Cov.: 29

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.870 AC: 132328 AN: 152062 Hom.: 57967 Cov.: 29 AF XY: 0.872 AC XY: 64783 AN XY: 74334

African (AFR) AF: 0.821 AC: 34031 AN: 41446

American (AMR) AF: 0.784 AC: 11945 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2930 AN: 3470

East Asian (EAS) AF: 0.729 AC: 3775 AN: 5178

South Asian (SAS) AF: 0.958 AC: 4611 AN: 4814

European-Finnish (FIN) AF: 0.967 AC: 10247 AN: 10598

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.911 AC: 61974 AN: 68002

Other (OTH) AF: 0.843 AC: 1782 AN: 2114

Alfa AF: 0.901 Hom.: 31762

Bravo AF: 0.852

Asia WGS AF: 0.861 AC: 2997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.75
PhyloP100		0.50
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2513046; hg19: chr11-62236094;